Miracle-dz/UniFAR-FTUs huggingface dataset:
WEdiff: A Python and C++ package for automatic differentiation

The need to calculate derivatives occurs frequently in the development of codes that do numerical computations. A common example is codes that solve ordinary or partial differential differential equations, where differentiation may be required for linearization or for determining the sensitivity of the solution to input parameters. There are a wide variety of methods available to calculate numerical derivatives, including finite differences. Although finite differences can be useful, they are prone to various errors including truncation error (when the difference between the function values is too large) and cancellation error (when the difference between the function values is too small) (Griewank & Walther, 2008). Automatic differentiation is a technique that is able to calculate derivatives with machine accuracy by systematically propagating derivatives through the code using the chain rule of calculus. Essentially, the algorithm is viewed simply as a large number of differentiable operations on data, i.e., the composition of the functions f0, f1, . , fn, for which the derivative with respect to the first function value (which may be a constant) is:
Performance Evaluation of Xen, KVM, and Proxmox Hypervisors

Hardware﻿virtualization﻿plays﻿a﻿major﻿role﻿in﻿IT﻿infrastructure﻿optimization﻿in﻿private﻿data﻿centers﻿and﻿ public﻿cloud﻿platforms. ﻿Though﻿there﻿are﻿many﻿advancements﻿in﻿CPU﻿architecture﻿and﻿hypervisors﻿ recently,﻿but﻿overhead﻿still﻿exists﻿as﻿there﻿is﻿a﻿virtualization﻿layer﻿between﻿the﻿guest﻿operating﻿system﻿ and﻿physical﻿hardware. ﻿This﻿is﻿particularly﻿when﻿multiple﻿virtual﻿guests﻿are﻿competing﻿for﻿resources﻿ on﻿the﻿same﻿physical﻿hardware. ﻿Understanding﻿performance﻿of﻿a﻿virtualization﻿layer﻿is﻿crucial﻿as﻿this﻿ would﻿have﻿a﻿major﻿impact﻿on﻿entire﻿IT﻿infrastructure. ﻿This﻿article﻿has﻿performed﻿an﻿extensive﻿study﻿ on﻿comparing﻿the﻿performance﻿of﻿three﻿hypervisors﻿KVM,﻿Xen,﻿and﻿Proxmox﻿VE. ﻿The﻿experiments﻿ showed﻿that﻿KVM﻿delivers﻿ the﻿best﻿performance﻿on﻿most﻿of﻿ the﻿selected﻿parameters. ﻿Xen﻿excels﻿ in﻿file﻿system﻿performance﻿and﻿application﻿performance. ﻿Though﻿Proxmox﻿has﻿delivered﻿the﻿best﻿ performance﻿in﻿only﻿the﻿sub-category﻿of﻿CPU﻿throughput. ﻿This﻿article﻿suggests﻿best-suited﻿hypervisors﻿ for﻿targeted﻿applications. KEywORdS Cloud Computing, Hypervisor, Performance, Virtualization
As-global-as-possible stereo matching with adaptive smoothness prior

More global matching (MGM) overcomes the limitation of one-dimensional scanline optimisation in semi-global matching (SGM). Nevertheless, the possible weaknesses of the MGM algorithm are as follows: (i) only two directions are considered for each image traversal direction, which may lead to massive mismatches; (ii) disparity estimation around the object boundaries usually performs terrible since the smoothness term is designed independent of the image prior. In this research, the authors consider all of the four directions for each image traversal direction through a novel model. Besides utilising the prior of neighboured pixels' correlation, adaptive smoothness terms are modelled and augmented into the energy function. These contributions encourage `as-global-as-possible (AGAP)'. More importantly, different from the recent works in which the aggregated algorithms have been conducted as the data term of an energy function, conversely, the authors make the energy function as a part of cost aggregation framework. Performance evaluations on Middlebury v.2 and v.3 stereo data sets demonstrate that the proposed AGAP outperforms other four most challenging stereo matching algorithms, and also performs better on Microsoft i2i stereo videos. In addition, under various strategies of parallelisation, the presented AGAP shows a near real-time execution time.
Role of MDM2 309T>G (rs2279744) and I/D (rs3730485) polymorphisms and haplotypes in risk of papillary thyroid carcinoma, tumor stage, tumor size, and early onset of tumor: A case control study

Murine double minute clone 2 (MDM2) protein plays an important role in the regulation of p53 tumor suppressor. Genetic polymorphisms of the MDM2 gene are the candidate variants in susceptibility to various cancers. In the present study, we aimed to investigate the possible effects of MDM2 309T>G (rs2279744) and I/D (rs3730485) polymorphisms on papillary thyroid carcinoma (PTC) susceptibility and clinical or pathological features of the disease. A case control study was carried out involving in a total of 131 patients with PTC and 144 healthy controls. Both cases and controls were genotyped for MDM2 309T>G and I/D polymorphisms. There was no significant difference regarding MDM2 309T>G and I/D genotypes between patients with PTC and controls in neither dominant nor recessive and allelic models. The frequency of G‐D haplotype was higher in patients with PTC and this haplotype was associated with a 1.7‐fold increased risk of PTC. The MDM2 309T>G polymorphism was associated with a higher risk of III–IV stages in patients with PTC. The MDM2 ID genotype was significantly higher in patients with PTC less than 40 years and associated with larger tumor size (≥1 cm). In conclusion, the G‐D haplotype but not MDM2 309T>G and I/D polymorphisms were associated with higher risk of PTC. MDM2 309T>G polymorphism was associated with a higher incidence of III–IV stages, however, I/D polymorphism was associated with larger tumor size and a lower age of disease occurrence.
Efficient coarser-to-fine holistic traffic sign detection for occlusion handling

In this study, the authors present a new efficient method based on discriminative patches (d-patches) for holistic traffic sign detection with occlusion handling. Traffic sign detection is an important part in autonomous driving, but usually hampered by the occlusions encountered on roads. They propose a method which basically upgrades d-patches by integrating vocabulary learning features. Consequently, d-patches are more discriminatively trained for robust occlusion handling. In addition, a holistic classifier is trained on d-patches, which identify those regions where occlusion exists. This results in higher confidence-score for the regions which contain traffic signs and lower confidence-score for the regions containing occlusions. Furthermore, they also propose a new coarser-to-fine (CTF) approach to speed up the traffic sign detection process. CTF minimises the use of traditional sliding window for object detection. It relies on colour variance to search the regions with high probability of traffic sign presence. Sliding window is used only on the selected high probability regions. The proposed method achieves 100% detection results on German Traffic Sign Detection Benchmark and performs 2.2% better than the previous state-of-the-art methods on Korean Traffic Sign Detection dataset, under partially occluded settings. By using CTF approach, five times speedup with a marginal loss in accuracy can be achieved.
The Choreographic Interface: Dancing Facial Expression in Hip-Hop and Neo-Burlesque Striptease

Although the face possesses potent social and symbolic meaning, the “dancing face” is rarely addressed in dance scholarship. In spite of its neglect, the face participates choreographically in the realization of aesthetic codes and embodied conventions that pertain to different dance styles and genres. I therefore turn to Gilles Deleuze and Felix Guattari's (1987) theory of “faciality” to understand the semiotic coding of the face in relation to the Busby Berkeley chorus girl. Although their work offers an important critique of universalist theorizations of facial expression, I argue that “facial choreography” offers scope to dismantle the legibility of the face that is produced through the overcoded “abstract machine of faciality. ” To do so, I introduce the concept of a “choreographic interface” to explore how facial expression enters into a choreographic relationship with other faces and bodily territories. With this in mind, I explore two dancing bodies that engage the face in ways that complicate existing modalities of facial expression. I analyze a hip-hop battle and a neo-burlesque striptease number to show how the mobility and ambiguity of facial choreography opens a dialogic space through which meaning is generated and social and political critique take place.
Fractional crow search-based support vector neural network for patient classification and severity analysis of tuberculosis

The world is chasing towards the automation in the severity analysis and classification of the patients based on the severity of tuberculosis (TB). The automatic classification is very much useful for developing countries that are struggling to reduce the fatality rate of the persons suffering from TB as it is a top standing infectious disease. Thus, the automatic classification of the TB patients using the sputum images with the proposed fractional crow search-based support vector neural network is presented. The proposed classification method is the integration of the fractional theory in the crow search algorithm that increases the computational speed and reduces the cost and time spent on analysing the test samples. The importance of the proposed method is that it requires minimum manual power and hence, the inaccuracies are reduced. The experimentation performed using the Ziehl-Neelsen sputum smear microscopy image database proves that the proposed classifier is highly accurate and offered an improved performance in terms of accuracy rate, true positive rate, and false-positive rate.
Analysis of the Transcriptome of the Red Seaweed Grateloupia imbricata with Emphasis on Reproductive Potential

Grateloupia imbricata is an intertidal marine seaweed and candidate model organism for both industry and academic research, owing to its ability to produce raw materials such as carrageenan. Here we report on the transcriptome of G. imbricata with the aim of providing new insights into the metabolic pathways and other functional pathways related to the reproduction of Grateloupia species. Next-generation sequencing was carried out with subsequent de novo assembly and annotation using state-of-the-art bioinformatic protocols. The results show the presence of transcripts required for the uptake of glycerol, which is a specific carbon source for in vitro culture of G. imbricata and nucleotide sequences that are involved in polyamine-based biosynthesis, polyamine degradation, and metabolism of jasmonates and ethylene. Polyamines, ethylene and methyl jasmonate are plant growth regulators that elicit the development and maturation of cystocarps and the release of spores from seaweeds. Our results will inform studies of the mechanisms that control polysaccharide accumulation, cystocarp formation and spore release. Moreover, our transcriptome information clarifies aspects of red seaweed carposporogenesis with potential benefits for enhancing reproduction.
Defining the complement C3 binding site and the antigenic region of Haemonchus contortus GAPDH

Haemonchus contortus is an economically important parasite that survives the host defense system by modulating the immune response. Glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) is secreted by the parasite and the host responds by producing anti‐enzyme antibodies. The enzyme inhibits complement cascade, an arm of the innate immunity, by binding to complement C3. In this study, the C3 binding site and the antigenic region of the enzyme were identified by generating short recombinant fragments and deleting a defined region of the enzyme. Using these proteins in ligand overlay and plate binding assay, the C3 binding region of GAPDH was localized within the 38 residues represented by 77‐114 amino acids whereas one of the antigenic regions was identified in between 77 and 171 amino acids. In addition, deletion of amino acids 77 to 171 from GAPDH (fragment AB) also showed weak immunogenicity but lacked C3 binding activity. Fragment D comprising 95 residues (77‐171), had both the C3 binding activity as well as immunogenicity like the parent enzyme, also stimulated host peripheral blood mononuclear cells in vitro. This truncated GAPDH moiety was stable at refrigerated temperature for at least 12 weeks and appears as a promising new therapeutic tool considering its longer shelf life as compared to the parent protein.
A New Cytotoxic Stigmasterone from Agathis Macrophylla

A new stigmasterone 7α,15α-dihydroxystigmast-4-en-3-one (1), along with fifteen known compounds was isolated from the EtOAc and n-BuOH fractions of the EtOH extract of Agathis macrophylla. The structure of these compounds 1-16 were established mainly by spectroscopic analysis and by comparison of the spectroscopic data with those reported for structurally related compounds. The isolated compounds 1-8 were screened for cytotoxicity in A549 tumor cell line using RSB assay. Compounds 1 and 2 displayed moderate cytotoxicity against A549 tumor cell line with IC50 value of 36.5 and 16.0 μmol/L, respectively.
Use of 18F-FDG PET/CT Imaging for Radiotherapy Target Volume Delineation after Induction Chemotherapy and for Prognosis of Locally Advanced Squamous Cell Carcinoma of the Head and Neck

Background and objectives: Induction chemotherapy (ICT) before definitive chemoradiation (CRT) gives high response rates in locally advanced squamous cell carcinoma of the head and neck (LA-SCCHN). However, pre-ICT gross tumor volume (GTV) for radiotherapy (RT) planning is still recommended. As 18F-FDG PET/CT has an advantage of biological tumor information comparing to standard imaging methods, we aimed to evaluate the feasibility of 18F-FDG PET/CT-based post-ICT GTV delineation for RT planning in LA-SCCHN and to assess the prognostic value of PET parameters: maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV) and total lesion glycolysis (TLG). Methods: 47 LA-SCCHN patients were treated with 3 cycles of ICT (docetaxel, cisplatin, and 5-fluorouracil) followed by CRT (70 Gy in 35 fractions with weekly cisplatin). Pre- and post-ICT PET/CT examinations were acquired. Planning CT was co-registered with post-ICT PET/CT and RT target volumes were contoured according to post-ICT PET. Post-ICT percentage decrease of SUVmax, MTV and TLG in primary tumor and metastatic regional lymphnodes (LN) was counted. Loco-regional failure patterns, 3-year progression free (PFS) and overall survival (OS) were evaluated. Results: 3-year PFS and OS rates for study population were 67% and 61% respectively. 31.9% of patients progressed loco-regionally. All progress was localized in high-to-intermediate dose (60–70 Gy) RT volumes and none in low dose (50 Gy) volumes. Decrease of SUVmax ≥ 74% (p = 0.04), MTV ≥ 68% (p = 0.03), TLG ≥ 76% (p = 0.03) in primary tumor, and LN TLG decrease ≥ 74% (p = 0.03) were associated with PFS. Decrease of primary tumor SUVmax ≥ 74% (p = 0.04), MTV ≥ 69% (p = 0.03), TLG ≥ 74% (p = 0.02) and LN TLG ≥ 73% (p = 0.02) were prognostic factors for OS. Conclusions: According to our results, 18F-FDG PET/CT-based post-ICT GTV delineation is feasible strategy without negative impacts on loco-regional control and survival. Percentage decrease of metabolic PET parameters SUVmax, MTV and TLG has a prognostic value in LA-SCCHN.
Health coaching and motivational interviewing: Evaluating the chronic disease self-management toolbox as a tool for person-centered healthcare

Objective: Many tools have been developed to assist patients in the self-management of chronic disease. Despite the role of clinicians in guiding patients to positive health outcomes, there has been little investigation of the tools from their perspective. The aim of this study was to investigate the preferences and motivations with which health professionals use chronic disease self-management (CDSM) tools as vehicles to improve the person-centeredness of clinical care. Method: Data collection was conducted in three phases comprising key informant interviews, piloting of data collection materials and interviews with CDSM practitioners. Findings: Key informant interviews established a need to explore clinicians’ use of health coaching and motivational interviewing in CDSM. While all participants used multiple tools for CDSM, there was a strong preference for health coaching for its effectiveness, adaptability and strong applicability to CDSM. There was widespread use of motivational interviewing, yet it was the least preferred tool. A third tool, Acceptance and Commitment Therapy (ACT), was considered to produce positive outcomes by reducing patient barriers. However, it was of limited applicability to CDSM. Four themes emerged as determinants of clinicians’ tool preferences and use: (i) strengths and weaknesses; (ii) flexibility; (iii) skills and (iv) barriers to implementation. Conclusion: Beyond descriptions of individual tools, this study shows how health professionals adopt a ‘toolbox’ approach to tailor CDSM to their patients. Adaptable and flexible tools such as health coaching and motivational interviewing empower clinicians to meet the complex needs of people living with chronic disease and to increase the person-centeredness of clinical care. However, workplace and patient barriers continue to impact on the acquisition of patients’ self-management skills and the satisfaction of health professionals working to achieve better patient outcomes.
GPU-optimized hybrid neighbor/cell list algorithm for coarse-grained molecular dynamics simulations

vi Chapter 1 Overview of Supercomputing . 1 1.1 History of Supercomputing . 2 1.2 Supercomputing Milestones . 2 Chapter 2 Graphics Processing Units . 8 2.1 Computer Graphics Technology and Parallel Computations . 9 2.2 GPU Computing for General Purpose Programming . 10 2.3 General Purpose GPU Programming Languages . 11 2.3.1 CUDA for General Purpose GPU Programming . 11 2.3.2 GPU Programming Bottlenecks . 14 Chapter 3 Background on Molecular Dynamics . 16 3.1 Biomolecular Folding Processes . 17 3.2 Molecular Dynamics Algorithm . 17 3.3 Coarse-Grained Simulation Models . 21 3.4 Molecular Dynamics with GPUs . 22 Chapter 4 Background on Cutoff Methods. 24 4.1 Verlet Neighbor List Algorithm . 25 4.2 GPU-Optimized Parallel Neighbor List Algorithm . 27 4.3 Cell List Algorithm . 29 Chapter 5 GPU-Optimized Cell List and Hybrid Neighbor/Cell List Algorithms 32 5.1 Possible Implementations of the Cell List Algorithm on GPUs . 32 5.2 Parallel Cell List Algorithm . 33 5.3 Hybrid Neighbor/Cell List Algorithm . 35
Mucor chuxiongensis sp. nov., a novel fungal species isolated from rotten wood.

Three strains of a novel mucoralean fungus were isolated from samples of decayed wood, which were collected from three locations near the city of Chuxiong, Yunnan province, China. These isolates were identified as a novel species through comparison of sequences in the ITS sequence, the D1/D2 domains of the LSU rRNA gene, and other taxonomic characteristics. The results demonstrated that these isolates represent a novel mucoralean fungus species belonging to the genus Mucor. The ITS sequence of Mucor chuxiongensissp. nov. differed from its closest relative, Mucor guilliermondii CBS 174.27T, by 13.1 % sequence divergence (39 substitutions and 38 gaps), and the D1/D2 sequences of the novel strains differed by 13 nt substitutions and one gap (1.9 %) from the ex-type strain. On potato dextrose agar, malt extract agar and synthetic mucor agar, the isolates grew slowly below 10 °C, rapidly at 25-30 °C, and could not grow well at 35 °C. The holotype strain of Mucor chuxiongensis sp. nov. is NYNU 174111 (CICC 41666T=CBS 143707T).
Electrospun poly‐l‐lactic acid/polyvinyl alcohol nanofibers improved insulin‐producing cell differentiation potential of human adipose‐derived mesenchymal stem cells

Combination of adipose‐derived mesenchymal stem cells (ADSCs) and synthetic materials in terms of pancreatic tissue engineering can be considered as a treatment of diabetes. This study aimed to evaluate the differentiation of human ADSCs to pancreatic cells on poly‐l‐lactic acid/polyvinyl alcohol (PLLA/PVA) nanofibers as a three‐dimensional (3D) scaffold. Mesenchymal stem cells (MSCs) were characterized for mesenchymal surface markers by flow cytometry. Then ADSCs were seeded on 3D scaffolds and treated with pancreatic differentiation medium. Immunostaining assay showed that ADSCs were very efficiently differentiated into a relatively homogeneous population of insulin‐producing cells. Moreover, real‐time RT‐PCR results revealed that pancreas‐specific markers were highly expressed in 3D scaffolds compared with their expression in tissue culture plates and this difference in expression level was significant. In addition, insulin and C‐peptide secreted in response to varying concentrations of glucose in the 3D scaffold group was significantly higher than that in 2D culture. The results of the present study confirmed that PLLA/PVA scaffold seeded with ADSCs could be a suitable option in pancreatic tissue engineering.
Anti-CRISPR-Based and CRISPR-Based Genome Editing of Sulfolobus islandicus Rod-Shaped Virus 2

Genetic engineering of viruses has generally been challenging. This is also true for archaeal rod-shaped viruses, which carry linear double-stranded DNA genomes with hairpin ends. In this paper, we describe two different genome editing approaches to mutate the Sulfolobus islandicus rod-shaped virus 2 (SIRV2) using the archaeon Sulfolobus islandicus LAL14/1 and its derivatives as hosts. The anti-CRISPR (Acr) gene acrID1, which inhibits CRISPR-Cas subtype I-D immunity, was first used as a selection marker to knock out genes from SIRV2M, an acrID1-null mutant of SIRV2. Moreover, we harnessed the endogenous CRISPR-Cas systems of the host to knock out the accessory genes consecutively, which resulted in a genome comprised solely of core genes of the 11 SIRV members. Furthermore, infection of this series of knockout mutants in the CRISPR-null host of LAL14/1 (Δarrays) confirmed the non-essentiality of the deleted genes and all except the last deletion mutant propagated as efficiently as the WT SIRV2. This suggested that the last gene deleted, SIRV2 gp37, is important for the efficient viral propagation. The generated viral mutants will be useful for future functional studies including searching for new Acrs and the approaches described in this case are applicable to other viruses.
Patterns of Fashion: The Cut and Construction of Clothes for Men and Women C1560-1620

The third volume in Janet Arnold's groundbreaking series Patterns of Fashion covers an earlier period than the previous two volumes: Patterns of Fashion 1660-1860 and Patterns of Fashion 1860-1940, concentrating on the Elizabethan and Jacobean eras. Significantly, too, this is the first of Arnold's books to include patterns for men's clothing. As well as Janet Arnold's meticulous patterns for these remarkable garments, the book includes an amazing 300 black and white photographs ranging from portraits of the period to details of articles of clothing .
Review of algorithms changing image size

Abstract. Improvement in imaging technology, such as recording and showing the images, has occurred everywhere. To see them, different types of screens, like HD monitors or cell phones with LD screens, are used and images often should be resized, to be in accord with different screens. In recent years, there is special attention paid to the methods of resizing which are employed to better show the images in various applications. This article surveys and studies the methods of image resizing (organized images, content-aware techniques of image organization, seam carving, multi-operator method, multi-layer image pointing, sufficient capacity imaging method, and image retargeting).