Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural Star Domain as Primitive Representation

Reconstructing 3D objects from 2D images is a fundamental task in computer vision. Accurate structured reconstruction by parsimonious and semantic primitive representation further broadens its application. When reconstructing a target shape with multiple primitives, it is preferable that one can instantly access the union of basic properties of the shape such as collective volume and surface, treating the primitives as if they are one single shape. This becomes possible by primitive representation with unified implicit and explicit representations. However, primitive representations in current approaches do not satisfy all of the above requirements at the same time. To solve this problem, we propose a novel primitive representation named neural star domain (NSD) that learns primitive shapes in the star domain. We show that NSD is a universal approximator of the star domain and is not only parsimonious and semantic but also an implicit and explicit shape representation. We demonstrate that our approach outperforms existing methods in image reconstruction tasks, semantic capabilities, and speed and quality of sampling high-resolution meshes.
Efficient Generalized Spherical CNNs

Many problems across computer vision and the natural sciences require the analysis of spherical data, for which representations may be learned efficiently by encoding equivariance to rotational symmetries. We present a generalized spherical CNN framework that encompasses various existing approaches and allows them to be leveraged alongside each other. The only existing non-linear spherical CNN layer that is strictly equivariant has complexity $\mathcal{O}(C^2L^5)$, where $C$ is a measure of representational capacity and $L$ the spherical harmonic bandlimit. Such a high computational cost often prohibits the use of strictly equivariant spherical CNNs. We develop two new strictly equivariant layers with reduced complexity $\mathcal{O}(CL^4)$ and $\mathcal{O}(CL^3 \log L)$, making larger, more expressive models computationally feasible. Moreover, we adopt efficient sampling theory to achieve further computational savings. We show that these developments allow the construction of more expressive hybrid models that achieve state-of-the-art accuracy and parameter efficiency on spherical benchmark problems.
Correlation between smoking and neovascularization in biceps tendinopathy: a functional preoperative and immunohistochemical study

Aims: The purpose of this study was to investigate whether smoking is associated with neovascularization in the tendinopathy of the long head of the biceps tendon (LHBT). Methods: The study included 40 consecutive patients who underwent arthroscopic biceps tenotomy/tenodesis due to chronic biceps tendinopathy and divided into three groups: (1) non-smokers, (2) former smokers, (3) smokers. LHBT tissue samples were stained with H&E, Alcian blue and Trichrome staining. Immunohistochemical examination was performed using anti-CD31 and anti-CD34. The neovessel density score (NDS) was scored by Bonar criteria. Results: The mean period of smoking was 15.50 years with an average number of 24 cigarettes/day in the former smokers and 21.69 years with an average number of 15 cigarettes/day in the active smokers. The mean NDS was 2.23/3 in non-smokers, whereas it was 1.60/3 in former smokers and 1.31/3 in active smokers. The mean American Shoulder and Elbow Surgeons score equaled 46 in never smoked patients, 43.60 in former smokers, and 41.46 in active smokers. In the patients with smoking history, the disorganized tendinous tissue islands were avascular and composed of compact acidic polysaccharides and mucopolysaccharides. We observed negative correlation between the NDS and the smoking indexes, including cigarettes per day (p = 0.0150), smoking years (p = 0.0140), pack-years (p = 0.0088). Conclusion: In conclusion, the present study revealed that smoking impairs the vascularization of the biceps tendon in chronic tendinopathy. Clinically, we observed a negative correlation between smoking and neovascularization. Furthermore, there was no correlation between neovascularization and functional preoperative status.
Prediction of the infection of COVID-19 in Bangladesh by classical SIR model

The ongoing outbreak of the novel coronavirus (COVID-19) started from Wuhan, China, at the end of December 2019. It is one of the leading public health challenges in the world because of high transmissibility. The first patient of COVID-19 was officially reported on March 8, 2020, in Bangladesh. Using the epidemiological data up to October 17, 2020, we try to estimate the infectious size. In this paper, we used Classical SIR (Susceptible- Infected-Recovered), model. The epidemic has now spread to more than 216 countries around the world. The necessary reproduction number R_o of Bangladesh is 1.92. The primary data was collected from the Coronavirus (COVID-19) Dashboard (BANGLADESH: CASE TREND). In our analysis, the statistical parameters specify the best import to provide the predicted result. We projected that the epidemic curve pulling down in Bangladesh will start from the first week of November (November 4, 2020) and may end in the last week of July (July 24, 2021). It is also estimated that the start of acceleration on May 24, 2020, in 53 days, and the start of steady growth on September 10, 2020, in 109 days. The start of the ending phase of the epidemic may appear in the first week of November 2020, and the epidemic is expected to be finished by the last week of July 2021. However, these approximations may become invalid if a large variety of data occurs in upcoming days.
Is screening for Cushing's syndrome before bariatric surgery necessary?

Purpose: Recent studies have shown a higher prevalence of Cushing's syndrome in obese patients with type 2 diabetes, but its prevalence in overweight and obese populations is not clear. The aim of this study was to evaluate the need for screening tests for Cushing's syndrome in morbidly obese individuals before bariatric surgery. Materials and methods: Between January 2015 and December 2019, 300 patients with Body Mass Index (BMI) ≥35 kg/m 2 that admitted to our endocrine outpatient clinic for evaluation before bariatric surgery were included in this study. Overnight low dose 1 mg dexamethasone suppression test was applied to all patients. Next day 8 am serum cortisol concentration less than 1.8 μg/dL was defined as normal suppression. Results: Three hundred patients undergoing bariatric surgery were screened for Cushing's syndrome. The mean ± standard deviation age of the patients was 39.4±11.7 years and 236 (77.3%) were women. The mean BMI of the patients was 45.9±5.5 kg/m 2 before bariatric surgery. Forty-seven (15.7%) patients in type 2 diabetes mellitus, 28 (9.3%) patients with hypertension and 3 (1%) patients who had achived euthyroidism after levothyroxine treatment. The mean one year BMI after bariatric surgery was 28±4.6 kg/m 2 . Serum cortisol concentration was <1.8 μg/dL after 1 mg overnight dexamethasone suppression test in all patients. Conclusion: The results of the evaluated data revealed that the routine screening of morbidly obese individuals for Cushing's syndrome before bariatric surgery is not necessary.
How the Internet reacted to Covid-19: A perspective from Facebook's Edge Network

The Covid-19 pandemic has led to unprecedented changes in the way people interact with each other, which as a consequence has increased pressure on the Internet. In this paper we provide a perspective of the scale of Internet traffic growth and how well the Internet coped with the increased demand as seen from Facebooks edge network. We use this infrastructure serving multiple large social networks and their related family of apps as vantage points to analyze how traffic and product properties changed over the course of the beginning of the Covid-19 pandemic. We show that there have been changes in traffic demand, user behavior and user experience. We also show that different regions of the world saw different magnitudes of impact with predominantly less developed regions exhibiting larger performance degradations.
Transcriptome Analysis of Vaccine Responses to Francisella Tularensis or Venezuelan Equine Encephalitis Virus

Transcriptome Analysis of Vaccine Responses to Francisella Tularensis or Venezuelan Equine Encephalitis Virus by Rebecca A. Erwin-Cohen MS, Hood College, 1995 BS, Gannon University, 1990 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Public Health -Epidemiology
Technology footprints in scientific discovery: Citation contexts of paper‐to‐patent citations

Citations between papers and patents indicate knowledge transfer between science and technology. This study discusses the function of paper‐to‐patent citations through citation contexts. 7,223 articles having at least one paper‐to‐patent citation are identified from a collection of 2.4 million PubMed Central open access articles. Within 429,698 references cited by the 7,223 articles, 11,165 (2.6%) are paper‐to‐patent citations, while 418,533 (97.4%) are paper‐to‐paper citations. In comparison to paper‐to‐paper citations, paper‐to‐patent citations were more concentrated at the beginning of articles. Higher proportions of patents are cited in the introduction and methods sections and are only cited once. The results indicate that patents are likely to be cited for providing background knowledge. The appearance of paper‐to‐patent citations in the method sections implies that patents might also contribute to the development of research methods.
Measures of Adult Shoulder Function

In the first systematic review of randomized controlled trials evaluating efficacy of interventions for shoulder pain published in 1998, none of the 31 included trials utilized a measure of function (1). Since then, at least 50 instruments to measure adult shoulder function have been developed and used in trials for shoulder pain (2). A 2011 review of nine of these tools, chosen based on having been cited in at least 20 references and for which psychometric testing had been reported, was published in a special issue of this journal devoted to patient outcome measures relevant to rheumatology (3). This updated review includes six of these nine tools and three new tools. Eight were chosen on the basis of being the most commonly used in randomized controlled trials in the last 5 years that were identified by searching Ovid MEDLINE and Ovid EMBASE from 2015 through December 9, 2019, using search strategies developed by Cochrane Musculoskeletal to identify common shoulder disorders, combined with Cochrane’s highly sensitive search strategies for randomized controlled trials. We also included Patient-Reported Outcomes Measurement Information System (PROMIS) Physical Function (PF) and Upper Extremity Computerized Adaptive Tests (CATs). Studies evaluating the measurement properties of the nine tools in shoulder conditions were identified by combining the relevant tool and search terms for common shoulder disorders with a search filter developed by Terwee et al for identifying such studies (4). There have been many psychometric studies of our chosen measures of adult shoulder function since the 2011 review. Many of the tools have been cross-culturally adapted into multiple languages, and these studies also provide important information regarding psychometric properties. Our review summarizes the available information about how these measures perform for different patient populations in different settings.
Aberrant DNA Methylation in Esophageal Squamous Cell Carcinoma: Biological and Clinical Implications

Almost all cancer cells possess multiple epigenetic abnormalities, which cooperate with genetic alterations to enable the acquisition of cancer hallmarks during tumorigenesis. As the most frequently found epigenetic change in human cancers, aberrant DNA methylation manifests at two major forms: global genomic DNA hypomethylation and locus-specific promoter region hypermethylation. It has been recognized as a critical contributor to esophageal squamous cell carcinoma (ESCC) malignant transformation. In ESCC, DNA methylation alterations affect genes involved in cell cycle regulation, DNA damage repair, and cancer-related signaling pathways. Aberrant DNA methylation patterns occur not only in ESCC tumors but also in precursor lesions. It adds another layer of complexity to the ESCC heterogeneity and may serve as early diagnostic, prognostic, and chemo-sensitive markers. Characterization of the DNA methylome in ESCC could help better understand its pathogenesis and develop improved therapies. We herein summarize the current research and knowledge about DNA methylation in ESCC and its clinical significance in diagnosis, prognosis, and treatment.
Integration of Online Omics-Data Resources for Cancer Research

The manifestations of cancerous phenotypes necessitate alterations at different levels of information-flow from genome to proteome. The molecular alterations at different information processing levels serve as the basis for the cancer phenotype to emerge. To understand the underlying mechanisms that drive the acquisition of cancer hallmarks it is required to interrogate cancer cells using multiple levels of information flow represented by different omics – such as genomics, epigenomics, transcriptomics, and proteomics. The advantage of multi-omics data integration comes with a trade-off in the form of an added layer of complexity originating from inherently diverse types of omics-datasets that may pose a challenge to integrate the omics-data in a biologically meaningful manner. The plethora of cancer-specific online omics-data resources, if able to be integrated efficiently and systematically, may facilitate the generation of new biological insights for cancer research. In this review, we provide a comprehensive overview of the online single- and multi-omics resources that are dedicated to cancer. We catalog various online omics-data resources such as The Cancer Genome Atlas (TCGA) along with various TCGA-associated data portals and tools for multi-omics analysis and visualization, the International Cancer Genome Consortium (ICGC), Catalogue of Somatic Mutations in Cancer (COSMIC), The Pathology Atlas, Gene Expression Omnibus (GEO), and PRoteomics IDEntifications (PRIDE). By comparing the strengths and limitations of the respective online resources, we aim to highlight the current biological and technological challenges and possible strategies to overcome these challenges. We outline the available schemes for the integration of the multi-omics dimensions for stratifying cancer patients and biomarker prediction based on the integrated molecular-signatures of cancer. Finally, we propose the multi-omics driven systems-biology approaches to realize the potential of precision onco-medicine as the future of cancer research. We believe this systematic review will encourage scientists and clinicians worldwide to utilize the online resources to explore and integrate the available omics datasets that may provide a window of opportunity to generate new biological insights and contribute to the advancement of the field of cancer research.
The Role of Gamma-Delta T Cells in Diseases of the Central Nervous System

Gamma-delta (γδ) T cells are a subset of T cells that promote the inflammatory responses of lymphoid and myeloid lineages, and are especially vital to the initial inflammatory and immune responses. Given the capability to connect crux inflammations of adaptive and innate immunity, γδ T cells are responsive to multiple molecular cues and can acquire the capacity to induce various cytokines, such as GM-CSF, IL-4, IL-17, IL-21, IL-22, and IFN-γ. Nevertheless, the exact mechanisms responsible for γδ T cell proinflammatory functions remain poorly understood, particularly in the context of the central nervous system (CNS) diseases. CNS disease, usually leading to irreversible cognitive and physical disability, is becoming a worldwide public health problem. Here, we offer a review of the neuro-inflammatory and immune functions of γδ T cells, intending to understand their roles in CNS diseases, which may be crucial for the development of novel clinical applications.
Host Cell Targets of Released Lipid and Secreted Protein Effectors of Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) is a very successful pathogen, strictly adapted to humans and the cause of tuberculosis. Its success is associated with its ability to inhibit host cell intrinsic immune responses by using an arsenal of virulence factors of different nature. It has evolved to synthesize a series of complex lipids which form an outer membrane and may also be released to enter host cell membranes. In addition, secreted protein effectors of Mtb are entering the host cell cytosol to interact with host cell proteins. We briefly discuss the current model, involving the ESX-1 type seven secretion system and the Mtb lipid phthiocerol dimycoserosate (PDIM), of how Mtb creates pores in the phagosomal membrane to allow Mtb proteins to access to the host cell cytosol. We provide an exhaustive list of Mtb secreted proteins that have effector functions. They modify (mostly inhibit but sometimes activate) host cell pathways such as: phagosome maturation, cell death, cytokine response, xenophagy, reactive oxygen species (ROS) response via NADPH oxidase 2 (NOX2), nitric oxide (NO) response via NO Synthase 2 (NOS2) and antigen presentation via MHC class I and class II molecules. We discuss the host cell targets for each lipid and protein effector and the importance of the Mtb effector for virulence of the bacterium.
Comparative Genomics of Plasmid-Bearing Staphylococcus aureus Strains Isolated From Various Retail Meats

Food poisoning due to the consumption of Staphylococcus aureus contaminated food is a major health problem worldwide. In this study, we sequenced the genomes of ten plasmid-bearing S. aureus strains isolated from retail beef, chicken, turkey, and pork. The chromosomes of the strains varied in size from 2,654,842 to 2,807,514 bp, and a total of 25 plasmids were identified ranging from 1.4 to 118 kb. Comparative genomic analysis revealed similarities between strains isolated from the same retail meat source, indicating an origin-specific genomic composition. Genes known to modulate attachment, invasion, and toxin production were identified in the 10 genomes. Strains from retail chicken resembled human clinical isolates with respect to virulence factors and genomic islands, and retail turkey and pork isolates shared similarity with S. aureus from livestock. Most chromosomes contained antimicrobial resistance, heavy metal resistance, and stress response genes, and several plasmids contained genes involved in antimicrobial resistance and virulence. In conclusion, the genomes of S. aureus strains isolated from retail meats showed an origin-specific composition and contained virulence and antimicrobial resistance genes similar to those present in human clinical isolates.
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.
Exosomes as a Novel Approach to Reverse Osteoporosis: A Review of the Literature

Osteoporosis is a chronic disease requiring long-term, sometimes lifelong, management. With the aging population, the prevalence of osteoporosis is increasing, and with it so is the risk of hip fracture and subsequent poor quality of life and higher mortality. Current therapies for osteoporosis have various significant side effects limiting patient compliance and use. Recent evidence has demonstrated the significant role of exosomes in osteoporosis both in vivo and in vitro. In this review, we summarize the pathogenesis of senile osteoporosis, highlight the properties and advantages of exosomes, and explore the recent literature on the use of exosomes in osteogenesis regulation. This is a very helpful review as several exosomes-based therapeutics have recently entered clinical trials for non-skeletal applications, such as pancreatic cancer, renal transplantation, and therefore it is urgent for bone researchers to explore whether exosomes can become the next class of orthobiologics for the treatment of osteoporosis.