Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central

Science across all disciplines has become increasingly data-driven, leading to additional needs with respect to software for collecting, processing and analysing data. Thus, transparency about software used as part of the scientific process is crucial to understand provenance of individual research data and insights, is a prerequisite for reproducibility and can enable macro-analysis of the evolution of scientific methods over time. However, missing rigor in software citation practices renders the automated detection and disambiguation of software mentions a challenging problem. In this work, we provide a large-scale analysis of software usage and citation practices facilitated through an unprecedented knowledge graph of software mentions and affiliated metadata generated through supervised information extraction models trained on a unique gold standard corpus and applied to more than 3 million scientific articles. Our information extraction approach distinguishes different types of software and mentions, disambiguates mentions and outperforms the state-of-the-art significantly, leading to the most comprehensive corpus of 11.8 M software mentions that are described through a knowledge graph consisting of more than 300 M triples. Our analysis provides insights into the evolution of software usage and citation patterns across various fields, ranks of journals, and impact of publications. Whereas, to the best of our knowledge, this is the most comprehensive analysis of software use and citation at the time, all data and models are shared publicly to facilitate further research into scientific use and citation of software.
Joint Beam Training and Data Transmission Control for mmWave Delay-Sensitive Communications: A Parallel Reinforcement Learning Approach

Future communication networks call for new solutions to support their capacity and delay demands by leveraging potentials of the millimeter wave (mmWave) frequency band. However, the beam training procedure in mmWave systems incurs significant overhead as well as huge energy consumption. As such, deriving an adaptive control policy is beneficial to both delay-sensitive and energy-efficient data transmission over mmWave networks. To this end, we investigate the problem of joint beam training and data transmission control for mmWave delay-sensitive communications in this paper. Specifically, the considered problem is firstly formulated as a constrained Markov Decision Process (MDP), which aims to minimize the cumulative energy consumption over the whole considered period of time under delay constraint. By introducing a Lagrange multiplier, we transform the constrained MDP into an unconstrained one, which is then solved via a parallel-rollout-based reinforcement learning method in a data-driven manner. Our numerical results demonstrate that the optimized policy via parallel-rollout significantly outperforms other baseline policies in both energy consumption and delay performance.
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics

Pleiotropic SNPs are associated with multiple traits. Such SNPs can help pinpoint biological processes with an effect on multiple traits or point to a shared etiology between traits. We present PolarMorphism, a new method for the identification of pleiotropic SNPs from GWAS summary statistics. PolarMorphism can be readily applied to more than two traits or whole trait domains. PolarMorphism makes use of the fact that trait-specific SNP effect sizes can be seen as Cartesian coordinates and can thus be converted to polar coordinates r (distance from the origin) and theta (angle with the Cartesian x-axis). r describes the overall effect of a SNP, while theta describes the extent to which a SNP is shared. r and theta are used to determine the significance of SNP sharedness, resulting in a p-value per SNP that can be used for further analysis. We apply PolarMorphism to a large collection of publicly available GWAS summary statistics enabling the construction of a pleiotropy network that shows the extent to which traits share SNPs. This network shows how PolarMorphism can be used to gain insight into relationships between traits and trait domains. Furthermore, pathway analysis of the newly discovered pleiotropic SNPs demonstrates that analysis of more than two traits simultaneously yields more biologically relevant results than the combined results of pairwise analysis of the same traits. Finally, we show that PolarMorphism is more efficient and more powerful than previously published methods.
Improving Fairness for SSD Devices through DRAM Over-Provisioning Cache Management

Modern NVMe SSDs have been widely deployed in multi-tenant cloud computing environments or multi-programming systems. When multiple applications concurrently access one SSD hardware, unfairness within the shared SSD will slow down the application significantly and lead to a violation of service level objectives. However, traditional data cache management within SSDs mainly focuses on improving cache hit ratio, which causes data cache contention and sacrifices fairness among multiple applications. In this paper, we propose a DRAM-based Over-Provisioning (OP) cache management mechanism, named Justitia, to reduce data cache contention and improve fairness for modern SSDs. Justitia consists of two stages including Static-OP stage and Dynamic-OP stage. Through the novel OP mechanism in the two stages, Justitia reduces the max slowdown by 4.5x on average. At the same time, Justitia increases fairness by 20.6x and buffer hit ratio by 19.6% averagely, compared with the traditional shared mechanism.
Bone‐Conducted Speech Synthesis Based on Least Squares Method

In this paper, we present a methodology to synthesize bone‐conduced (BC) speech. Without relying on commonly used techniques for speech synthesis, we consider to transform air‐conducted (AC) speech into BC speech. An infinite impulse response (IIR) filter is explored for the transformation. From the concept of system identification, the least squares (LS) method is employed and the IIR filter is designed through the recorded AC and BC speech data. By experiments, it is shown that the BC speech synthesis method is satisfactory. Filter model, order selection and stability in the methodology are discussed and noise‐robustness gained by the BC speech synthesis is also investigated. © 2022 Institute of Electrical Engineers of Japan. Published by Wiley Periodicals LLC.
Continuous B- to A-Transition in Protein-DNA Binding - How Well Is It Described by Current AMBER Force Fields?

When DNA interacts with a protein, its structure often undergoes significant conformational adaptation. Perhaps the most common is the transition from canonical B-DNA towards the A-DNA form, which is not a two-state, but rather a continuous transition. The A- and B-forms differ mainly in sugar pucker P (north/south) and glycosidic torsion χ (high-anti/anti). The combination of A-like P and B-like χ (and vice versa) represents the nature of the intermediate states lying between the pure A- and B- forms. In this work, we study how the A/B equilibrium and in particular the A/B intermediate states, which are known to be over-represented at protein-DNA interfaces, are modeled by current AMBER force fields. Eight protein-DNA complexes and their naked (unbound) DNAs were simulated with OL15 and bsc1 force fields as well as an experimental combination OL15χOL3. We found that while the geometries of the A-like intermediate states in the molecular dynamics (MD) simulations agree well with the native X-ray geometries found in the protein-DNA complexes, their populations (stabilities) are significantly underestimated. Different force fields predict different propensities for A-like states growing in the order OL15 < bsc1 < OL15χOL3, but the overall populations of the A-like form are too low in all of them. Interestingly, the force fields seem to predict the correct sequence-dependent A-form propensity, as they predict larger populations of the A-like form in naked (unbound) DNA in those steps that acquire A-like conformations in protein-DNA complexes. The instability of A-like geometries in current force fields may significantly alter the geometry of the simulated protein-DNA complex, destabilize the binding motif, and reduce the binding energy, suggesting that refinement is needed to improve description of protein-DNA interactions in AMBER force fields.
Prospective Primary Teachers’ Professional Noticing in Non-formal Learning Environments: The Case of a Mathematics Fair

Research around mathematics teachers’ professional noticing has been largely contextualised by the formal setting of the classroom. In addressing the lack of relevant studies in non-formal learning environments, this paper draws on student teachers’ observations within a Mathematics Fair, which was part of a mathematics methods module of a primary education undergraduate programme. Working in pairs, 64 student teachers designed interactive mathematical games which upper primary school pupils had the opportunity to play in an event having taken place at our university. In this study, we analyse student teachers’ individual reflective essays written after the Fair, where they discussed important, in their view, incidents and observations. Employing a thematic analysis approach, we identified four themes discussed by students: the task; learning; teaching; non-formal environment. We conclude with the implications for teacher education and suggestions for future research.
Remote Water Quality Monitoring System Based on WSN and GPRS

To resolve the problem of the manual analytical method adopted in water quality detection with bad real-time character,this paper introduced a novel kind of remote water quality measuring and monitoring system based on WSN and GPRS network.It used wireless sensor network based on the Zombie and GPRS network to realize the water quality parameter remote probing and the real-time monitoring function.Users can observe the current or historical water quality status easily.And it provided a reasonable basis for the further breeding plan.This system has a simple architecture,and isn't confined by the geographical position.According to the test results,this system can run stably,and its operation is convenient.
A Search for Champion Boxers

Summary In the world of boxing, fighters are judged by the quality of their opponents. This way of determining value is reminiscent of Google’s PageRank algorithm, which assigns values to websites based on the value of sites linked to it. We describe the mathematics behind PageRank, and then offer a scheme for adaptingva it to boxing. We illustrate the behavior of this algorithm in several scenarios. We then select 20 top heavyweight boxers from the 1990’s and rank them using our method. A comparison is made to the Colley method of ranking. We conclude by describing some possible extensions of this method.
Convolutional‐capsule network for gastrointestinal endoscopy image classification

Automated diagnosis of digestive tract diseases from gastrointestinal endoscopy images is of high importance for improving the diagnosis accuracy and efficiency. The current mainstream methods for image classification of digestive tract endoscopy images are based on Convolutional Neural Networks (CNNs). However, due to their inherent defects, CNNs are not strong enough in learning deformation‐invariant global features which is essential in gastrointestinal endoscopic image classification. To solve this problem, in this paper we present a two‐stage endoscopic image classification method which can effectively combine complementary advantages of midlevel CNN features and a capsule network. Specifically, the core of our method is a lesion‐aware CNN feature extraction module which can encode sufficiently detailed information of lesions in midlevel CNN features and in turn enable the subsequent capsule classification network to effectively learn deformation‐invariant relationships between image entities. Extensive experiments demonstrate the superiority of our method to the state‐of‐the‐art methods with the classification accuracy of 94.83% on the Kvasir v2 data set and the classification accuracy of 85.99% on the HyperKvasir data set.
Method Study on Joint-design 2D Engineering Drawing Using ProE and autoCAD Software

Making use of powerful 3D design function of ProE software and powerful 2D design function of autoCAD software,the method of joint-design 2D engineering drawing using ProE and autoCAD software was analyzed by an example.Compared with designing the 2D engineering drawing in sole software,the joint-design is very swift.
The Unique Carboxymethyl Fenugreek Gum Gel Loaded Itraconazole Self-Emulsifying Nanovesicles for Topical Onychomycosis Treatment

The novel itraconazole (ITZ) nail penetration enhancing self-emulsifying nanovesicles (ITZ-nPEVs) loaded in carboxymethyl fenugreek gum (CMFG) gel circumvent the systemic onychomycosis treatment. The ITZ-nPEVs were prepared by the thin film hydration technique, and the particle size (PS), zeta potential (ZP), drug content (DC), entrapment efficiency (% EE), deformity index (DI), viscosity, morphology, and physical stability of the ITZ-nPEVs were measured. In terms of nail hydration, transungual drug absorption, and antifungal efficacy against Candida albicans, the chosen ITZ-nPEVs, nPEV-loaded CMFG (CMFG-ITZ-nPEVs) gel, and the commercialized Itrostred gel were compared. The ITZ-nPEVs showed spherical structure with high DC, % EE, low PS and PDI and positive ZP of ITZ ranging from 95.36 to 93.89 mg/5 mL and 95.36–96.94%, 196.55–252.5 nm, 0.092–0.49, and +11.1 to +22.5 mV, respectively. Compared to the Itrostred gel, the novel ITZ-nPEVs exhibited hydration enhancement factor for 24 h (HE24) of 1.53 and 1.39 drug uptake enhancement factor into nail clippings. Moreover, zone of inhibitions for ITZ-nPEVs (27.0 ± 0.25 mm) and CMFG-ITZ-nPEVs (33.2 ± 0.09 mm) against Candida albicans were significantly greater than that of Itrostred gel (22.9 ± 0.44 mm). For clinical investigation on onychomycotic patients, a nail penetration enhancer containing ITZ-nPEV-loaded CMFG gel presents a highly promising approach.
Towards Multi-Analyte Detection with Field-Effect Capacitors Modified with Tobacco Mosaic Virus Bioparticles as Enzyme Nanocarriers

Utilizing an appropriate enzyme immobilization strategy is crucial for designing enzyme-based biosensors. Plant virus-like particles represent ideal nanoscaffolds for an extremely dense and precise immobilization of enzymes, due to their regular shape, high surface-to-volume ratio and high density of surface binding sites. In the present work, tobacco mosaic virus (TMV) particles were applied for the co-immobilization of penicillinase and urease onto the gate surface of a field-effect electrolyte-insulator-semiconductor capacitor (EISCAP) with a p-Si-SiO2-Ta2O5 layer structure for the sequential detection of penicillin and urea. The TMV-assisted bi-enzyme EISCAP biosensor exhibited a high urea and penicillin sensitivity of 54 and 85 mV/dec, respectively, in the concentration range of 0.1–3 mM. For comparison, the characteristics of single-enzyme EISCAP biosensors modified with TMV particles immobilized with either penicillinase or urease were also investigated. The surface morphology of the TMV-modified Ta2O5-gate was analyzed by scanning electron microscopy. Additionally, the bi-enzyme EISCAP was applied to mimic an XOR (Exclusive OR) enzyme logic gate.
Snakes: Legal, Illegal and Dodecahedral

Summary We enumerate all Hamilton circuits on the dual graph of the dodecahedron, group them according to symmetry, and then discuss which of them may be realized as snake patterns on the Megaminx puzzle. We find that there are eleven shapes that may be obtained without taking the puzzle apart (legal shapes) and ten more that can be achieved if you swap two pieces (illegal). With color taken into account, there are 700 ways to put a snake on the Megaminx, 280 of them legal. Supplemental data for this article is available online at http://dx.doi. org/10.1080/0025570X.2022. 2001286
Parallel molecular mechanisms underlie convergent evolution of the exaggerated snout phenotype in East African cichlids

Studying instances of convergent evolution of novel phenotypes can shed light on the evolutionary constraints that shape morphological diversity. Cichlid fishes from the East African Great Lakes are a prime model to investigate convergent adaptations. However, most studies on cichlid craniofacial morphologies have primarily considered bony structures, while soft tissue adaptations have been less intensely scrutinised. A rare example of an exaggerated soft tissue phenotype is the formation of a snout flap. This tissue flap develops from the upper lip and has evolved in only one cichlid genus from Lake Malawi and one genus from Lake Tanganyika. To investigate the molecular basis of snout flap convergence, we used mRNA sequencing to compare two species with snout flap (Labeotropheus trewavasae and Ophthalmotilapia nasuta) to their close relatives without snout flaps (Tropheops tropheops and Ophthalmotilapia ventralis) from Lake Tanganyika and Malawi. Our analysis revealed a greater complexity of differential gene expression patterns underlying the snout flap in the younger adaptive radiation of Lake Malawi than in the older Lake Tanganyika radiation. We identified 201 genes that were repeatedly differentially expressed between species with and without the snout flap in both lakes, suggesting that the pathway that gives rise to snout flaps is evolutionarily constrained, even though the flaps play very different functions in each species. The convergently expressed genes are involved in proline and hydroxyproline metabolism, which have been linked to human skin and facial deformities. Additionally, we also found enrichment for transcription factor binding sites upstream of differentially expressed genes such as members of the FOX transcription factor family, especially foxf1 and foxa2, which also showed an increased expression in the flapped snout and are linked to nose morphogenesis in mammals, as well as ap4 (tfap4), a transcription factor showing reduced expression in the flapped snout with an unknown role in the development of craniofacial soft tissues. As genes involved in cichlids snout flap development are associated with many human mid-line facial dysmorphologies, our findings imply a conservation of genes involved in mid-line patterning across vastly distant evolutionary lineages of vertebrates. Significance statement The study of the evolution of similar physical traits across taxa can give insight into the molecular architecture underlying shared phenotypes. This has mostly been studied in bony structures, while soft tissue traits have been less intensely covered. We investigated the exaggerated snout in cichlid species from Lake Malawi and Lake Tanganyika and found that many genes involved in the development of the snout flap are also associated with mid-line dysmorphologies in humans, implying a conservation across distant vertebrate lineages.
Intercostal nerve blockade with liposomal bupivacaine reduces length of stay after video assisted thoracic surgery (VATS) lobectomy

Background Intercostal nerve blockade (INB) for thoracic surgery analgesia has gained popularity in practice, but evidence demonstrating its efficacy remains sparse and inconsistent. We investigated the effect of INB with standard bupivacaine (SB) with epinephrine versus liposomal bupivacaine (LB) versus a mixed solution of the two on postoperative pain control and outcomes in video assisted thoracoscopic lobectomy patients. Methods Since 2014, our practice has shifted from using INBs with SB with epinephrine, to LB, to a mix of the two as the central component of multimodal analgesia after video assisted thoracoscopic surgery. The blocks are performed in a standardized fashion under thoracoscopic visualization consecutively from two rib spaces above to two below the outermost incisions. We retrospectively compared all minimally invasive lobectomies performed at our institution between January 2014 and July 2018 by type of local anesthetic used for INB. We examined median length of stay (LOS), opioid utilization, and subjective pain scores [0–10]. Results Out of 302 minimally invasive lobectomy patients, 34 received SB with epinephrine, 222 received LB alone, and 46 received the mixed solution. LOS was almost a full day shorter in the LB group than in the SB group (34.8 vs. 56.5 hours, P=0.01). There was nearly 25% lower median total morphine equivalent utilization in the mixed solution cohort compared to the LB cohort (−7.1 mg, P=0.02). Additionally, IV morphine equivalent utilization was over 50% lower in the mixed solution group than in the SB with epinephrine group (−10.0 mg, P=0.03). Conclusions Our study is by far the largest (N=302) to compare types of local anesthetic used for INB within a uniform case population. The reductions in LOS and opiate utilization observed in our study among patients receiving LB-based formulations were both statistically and clinically significant.
Bone Mineral Density Changes in Long-Term Kidney Transplant Recipients: A Real-Life Cohort Study of Native Vitamin D Supplementation

Vitamin D insufficiency has been associated with reduced bone mineral density (BMD) in kidney transplant patients (KTRs). However, the efficacy of vitamin D supplementation on BMD remains poorly defined, especially for long-term KTRs. We aimed to investigate the effect of native vitamin D supplementation on the BMD of KTRs during a 2-year follow-up. Demographic, clinical, and laboratory data were collected. BMD was evaluated with standard DEXA that was performed at baseline (before vitamin D supplementation) and at the end of study period. BMD was assessed at lumbar vertebral bodies (LV) and right femoral neck (FN) by a single operator. According to WHO criteria, results were expressed as the T-score (standard deviation (SD) relative to young healthy adults) and Z-score (SD relative to age-matched controls). Osteoporosis and osteopenia were defined as a T-score ≤ −2.5 SD and a T-score < −1 and a > −2.5 SD, respectively. Based on plasma levels, 25-OH-vitamin D (25-OH-D) was supplemented as recommended for the general population. Data from 100 KTRs were analyzed. The mean study period was 27.7 ± 3.4 months. At study inception, 25-OH-D insufficiency and deficiency were recorded in 65 and 35 patients. At the basal DEXA, the percentage of osteopenia and osteoporosis was 43.3% and 18.6% at LV and 54.1% and 12.2% at FN, respectively. At the end of the study, no differences in the Z-score and T-score gains were observed. During linear mixed model analysis, native vitamin D supplementation was found to have a negative nitration with Z-score changes at the right femoral neck in KTRs (p < 0.05). The mean dose of administered cholecalciferol was 13.396 ± 7.537 UI per week; increased 25-OH-D levels were found (p < 0.0001). Either low BMD or 25-OH-vitamin D concentration was observed in long-term KTRs. Prolonged supplementation with 25-OH-D did not modify BMD, Z-score, or T-score.
Spatial Computing and Intuitive Interaction: Bringing Mixed Reality and Robotics Together

Spatial computing—the ability of devices to be aware of their surroundings and to represent this digitally—offers novel capabilities in human–robot interaction. In particular, the combination of spatial computing and egocentric sensing on mixed reality (MR) devices enables robots to capture and understand human behaviors and translate them to actions with spatial meaning, which offers exciting possibilities for collaboration between people and machines. This article presents several human–robot systems that utilize these capabilities to enable novel use cases: mission planning for inspection, gesture-based control, and immersive teleoperation. These works demonstrate the power of MR as a tool for human–robot interaction and the potential of spatial computing and MR to drive future developments.