Miracle-dz/UniFAR-FTUs huggingface dataset:
Seedability: optimizing alignment parameters for sensitive sequence comparison

Abstract Motivation Most sequence alignment techniques make use of exact k-mer hits, called seeds, as anchors to optimize alignment speed. A large number of bioinformatics tools employing seed-based alignment techniques, such as Minimap2, use a single value of k per sequencing technology, without a strong guarantee that this is the best possible value. Given the ubiquity of sequence alignment, identifying values of k that lead to more sensitive alignments is thus an important task. To aid this, we present Seedability, a seed-based alignment framework designed for estimating an optimal seed k-mer length (as well as a minimal number of shared seeds) based on a given alignment identity threshold. In particular, we were motivated to make Minimap2 more sensitive in the pairwise alignment of short sequences. Results The experimental results herein show improved alignments of short and divergent sequences when using the parameter values determined by Seedability in comparison to the default values of Minimap2. We also show several cases of pairs of real divergent sequences, where the default parameter values of Minimap2 yield no output alignments, but the values output by Seedability produce plausible alignments. Availability and implementation https://github.com/lorrainea/Seedability (distributed under GPL v3.0).
Improved YOLOv5 Network for Steel Surface Defect Detection

Steel surface defect detection is crucial for ensuring steel quality. The traditional detection algorithm has low detection probability. This paper proposes an improved algorithm based on the YOLOv5 model to enhance detection probability. Firstly, deformable convolution is introduced in the backbone network, and a traditional convolution module is replaced by deformable convolution; secondly, the CBAM attention mechanism is added to the backbone network; then, Focal EIOU is used instead of the CIOU loss function in YOLOv5; lastly, the K-means algorithm is used to cluster the Anchor box, and the Anchor box parameters that are more suitable for this paper are obtained. The experimental results show that using deformable convolution instead of traditional convolution can get more feature information, which is more conducive to the learning of the network. This paper uses the CBAM attention mechanism, and the heat map of the attention mechanism shows that the CBAM attention mechanism is beneficial for feature extraction. Focal EIOU is optimized in high and wide loss compared with the CIOU loss function, which accelerates the convergence of the model. The Anchor box is more favorable for feature extraction. The improved algorithm achieved a detection probability of 78.8% in the NEU-DET dataset, which is 4.3% better than the original YOLOv5 network, and the inference time of each image is only increased by 1 ms; therefore, the optimized algorithm proposed in this paper is effective.
Do timed up and go and five times sit to stand test outcomes correlate with trunk stability? A pilot-study

BACKGROUND: Five Times Sit to Stand (FTSS) and Timed Up and Go (TUG) are clinical tests in which performance is evaluated through completion time, which can be thought to reflect dynamic balance. Completion time in these tests, however, can be affected not only by balance stability but also by other important components, such as legs’ muscular strength and velocity. AIM: This investigation aimed to evaluate the correlation of completion times in these clinical tests and mediolateral (ML) balance stability measured through lower trunk accelerometry in older individuals. METHOD: Fifteen volunteers were evaluated, aged 60-86 years (M = 69.56±5.89 years). For TUG, we evaluated the conventional version of the test (TUGC), in addition to a dual task (TUGDT) and a new overline (TUGOL) version featured by increased balance demand. Balance stability during test performance was measured through ML accelerations of the lower trunk. RESULTS: The results indicated negative time-acceleration correlations for TUGC (rp = -.71, rp2 =.50, p <.01) and TUGDT (rp = -.77, rp2 =.59, p <.01) and a positive correlation for FTSS (rp =.73, rp2 =.53, p <.01). The TUGOL test failed to show significant time-acceleration correlations. CONCLUSION: Our results suggest that completion time in the FTSS test importantly reflects dynamic balance stability in older individuals. On the other hand, ML trunk acceleration when performing TUG seems to be more related to movement speed than body balance. Our results suggest that completion time can be considered a predictor of dynamic balance in the FTSS test.
Entity Resolution in Situated Dialog With Unimodal and Multimodal Transformers

In this work we address the entity resolution task for situated multimodal dialog investigating how a unimodal approach, which uses only textual information as input (representing visual attributes as text), compares to a multimodal system, which processes both text and visual information. We analyze two of the top performing models presented in the Tenth Dialog Systems Technology Challenge and propose modifications that enhance their performance on the multimodal coreference resolution task. We evaluate these approaches on in- and out-of-domain settings by training the models on the fashion domain and testing on the furniture domain, and vice-versa, to assess the generalizability of the models. Through systematic analysis, we show that while both systems achieve similar performance on in-domain scenarios, the multimodal system generalizes better to out-of-domain settings. A combination strategy of enhanced unimodal and multimodal systems achieves F1 = 0.80 (5% absolute gain compared to the best performing system). Finally, human performance on the same task is evaluated on a small subset, suggesting that the performance of the current automatic models is on par with people on this task.
A Performance Improvement for Indoor Positioning Systems Using Earth’s Magnetic Field

Although most indoor positioning systems use radio waves, such as Wi-Fi, Bluetooth, or RFID, for application in department stores, exhibition halls, stations, and airports, the accuracy of such technology is easily affected by human shadowing and multipath propagation delay. This study combines the earth’s magnetic field strength and Wi-Fi signals to obtain the indoor positioning information with high availability. Wi-Fi signals are first used to identify the user’s area under several kinds of environment partitioning methods. Then, the signal pattern comparison is used for positioning calculations using the strength change in the earth’s magnetic field among the east–west, north–south, and vertical directions at indoor area. Finally, the k-nearest neighbors (KNN) method and fingerprinting algorithm are used to calculate the fine-grained indoor positioning information. The experiment results show that the average positioning error is 0.57 m in 12-area partitioning, which is almost a 90% improvement in relation to that of one area partitioning. This study also considers the positioning error if the device is held at different angles by hand. A rotation matrix is used to convert the magnetic sensor coordinates from a mobile phone related coordinates into the geographic coordinates. The average positioning error is decreased by 68%, compared to the original coordinates in 12-area partitioning with a 30-degree pitch. In the offline procedure, only the northern direction data are used, which is reduced by 75%, to give an average positioning error of 1.38 m. If the number of reference points is collected every 2 m for reducing 50% of the database requirement, the average positioning error is 1.77 m.
Analysis of Factors Affecting Postoperative Opioid Requirement in Pediatric Patients Undergoing Pectus Excavatum Repair with Multimodal Analgesic Management

Children with pectus excavatum are treated with surgical repair in a procedure known as minimally invasive repair of pectus excavatum (MIRPE). MIRPE causes considerable postoperative pain, resulting in the administration of a substantial dose of opioids. This study aimed to identify perioperative factors that influence the requirement for opioids in children undergoing MIRPE. Retrospective data from children who underwent MIRPE were analyzed. A multimodal analgesic protocol was implemented with a continuous wound infiltration system and administration of non-opioid analgesics. Intravenous opioid analgesics were administered if the pain score was greater than 4. The cumulative opioid use was assessed by calculating the morphine equivalent dose at 6, 24, and 48 h after surgery. Perioperative factors affecting the postoperative opioid use were identified with multiple linear regression analyses. This study included 527 children aged 3–6 years, with a mean age of 3.9 years. Symmetrically depressed chest walls, a lower Haller index, and a lower revised depression index were found to be associated with decreased postoperative opioids. Boys required higher opioid doses than girls. Longer pectus bars (10 inches versus 9 inches) were associated with increased opioid use. Severity indices, gender, and the length of pectus bars influence postoperative opioid requirement in children undergoing MIRPE surgery with multimodal analgesia.
Game-theoretic Mechanisms for Eliciting Accurate Information

Artificial Intelligence often relies on information obtained from others through crowdsourcing, federated learning, or data markets. It is crucial to ensure that this data is accurate. Over the past 20 years, a variety of incentive mechanisms have been developed that use game theory to reward the accuracy of contributed data. These techniques are applicable to many settings where AI uses contributed data. This survey categorizes the different techniques and their properties, and shows their limits and tradeoffs. It identifies open issues and points to possible directions to address these.
Using a novel biologging approach to assess how different handling practices influence the post-release behaviour of Northern Pike across a wide range of body sizes

There is a growing body of research focused on how angled fish respond to catch-and-release (C&R). However, most of those studies do not span a wide range of body sizes for the targeted species. Physical injury and physiological responses to C&R can be size-dependent, and methods used for landing fish of different sizes vary. As such, studying the response to C&R across a range of fish sizes may help inform best practices that improve outcomes for released fish. Northern Pike (Esox lucius) widely ranges in body size. Anglers may land them by hand, cradle, or net, and they are often released voluntarily or to comply with regulations. We angled 25 Northern Pike (total length 620–1030 mm) from one population and recorded fight, handling, and unhooking times across landing methods (i.e., hand, cradle, net). Prior to release, a pop-off biologging package was temporarily affixed to each fish to monitor locomotor activity, depth, and water temperature during a 12-h period post-release to understand how the interaction of landing method and body size influenced post-release behaviour and short-term fate. Fight and handling time increased with increasing body size. Northern Pike landed with a cradle or net had shorter fight times but longer handling times, compared to fish landed by hand. Post-release locomotor activity was greater for larger fish and those landed with a net. Fish <775mm and landed by hand had greater locomotor activity than fish landed with a net or cradle, while fish >775mm landed by hand had reduced locomotor activity compared to fish landed with a net. There was no post-release mortality observed. Collectively, anglers should use a net for Northern Pike >775 mm to avoid long fight times and reduce post-release exhaustion, but also attempt to reduce the extent of handling associated with fish landed by net.
Characterization of the Heat Shock Transcription Factor Family in Medicago sativa L. and Its Potential Roles in Response to Abiotic Stresses

Heat shock transcription factors (HSFs) are important regulatory factors in plant stress responses to various biotic and abiotic stresses and play important roles in growth and development. The HSF gene family has been systematically identified and analyzed in many plants but it is not in the tetraploid alfalfa genome. We detected 104 HSF genes (MsHSFs) in the tetraploid alfalfa genome (“Xinjiangdaye” reference genome) and classified them into three subgroups: 68 in HSFA, 35 in HSFB and 1 in HSFC subgroups. Basic bioinformatics analysis, including genome location, protein sequence length, protein molecular weight and conserved motif identification, was conducted. Gene expression analysis revealed tissue-specific expression for 13 MsHSFs and tissue-wide expression for 28 MsHSFs. Based on transcriptomic data analysis, 21, 11 and 27 MsHSFs responded to drought stress, cold stress and salt stress, respectively, with seven responding to all three. According to RT–PCR, MsHSF27/33 expression gradually increased with cold, salt and drought stress condition duration; MsHSF6 expression increased over time under salt and drought stress conditions but decreased under cold stress. Our results provide key information for further functional analysis of MsHSFs and for genetic improvement of stress resistance in alfalfa.
A Novel Detection Method for Valve Damage of Nuclear Power Using Attention-Based U-Net (ABUNet)

The detection of valve seals is not only an essential part of the maintenance of nuclear power valves, but also a requirement for the safe, efficient, and cost-effective operation of nuclear power. A novel detection method for valve damage of nuclear power using attention-based U-Net (ABUNet) is proposed to detect damage location information on sealing surfaces of nuclear power valves. To better identify the damaged parts, an attention mechanism for damage characteristics is incorporated into the detection method. Datasets of four types of valve damage are established to identify different types of damage, and damage information extraction is introduced to verify the model’s capacity for identification. The index comparison with other models demonstrates the superiority of this network in valve damage identification. In contrast to other network structures for semantic segmentation, the model presented in this article offers some advantages in terms of accuracy and speed for detecting the sealing surface of nuclear power valves. The same damage dataset test verifies that the frequency weighted intersection over union (FWIoU) of ABUNet is 0.8049, which is about 0.05–0.13 higher than other segmentation approaches like fully convolutional network (FCN) and SegNet. Compared with the ABUNet with the same structure and different depths, the mean pixel accuracy (MPA) and mean intersection over union (MIoU) of the network with the depth of 5 are 0.9769 and 0.8239, respectively, which are 0.06–0.001 higher than the original U-net and the network with the depth of 3, 6, and 9. In addition, the detection time of ABUNet with depths of 5, 6, and 9, was 1.38, 1.45, and 1.72 s, respectively. From the comprehensive comparison results, the ABUNet with a depth of 5 is the best choice for detection results. Finally, examples are verified by actual pictures taken of valve damage.
The Clinical Variables Predicting the Acquisition of Independent Ambulation in the Acute Phase of Stroke: A Retrospective Study

Background: Predictive factors associated with independent ambulation post-stroke are less commonly reported for patients during the acute phase of stroke. This study aimed to identify the clinical variables predicting ambulation independence in the acute phase of stroke and test the superiority of their prediction accuracy. Methods: Sixty-nine patients, hospitalized in the acute phase for an initial unilateral, supratentorial stroke lesion, were divided into independent (n = 24) and dependent ambulation (n = 45) groups, with functional ambulation category scores of 4–5 and ≤ 3, respectively. They were evaluated upon admission using the modified Rankin scale (mRS), Stroke Impairment Assessment Set (SIAS) concerning the motor function of the lower extremities, Ability for Basic Movement Scale modified version 2 (ABMS2), and Functional Independence Measure (FIM). Results: The scores of the four measures were significantly different between the groups. A univariate logistic regression analysis identified these variables as prognostic factors for independent ambulation. A receiver operating characteristic curve analysis identified the cutoff values (area under the curve) for the mRS, SIAS, FIM, and ABMS2 as 3 (0.74), 12 (0.73), 55 (0.85), and 23 (0.84), respectively. Conclusion: In summary, the FIM and ABMS2 may be more accurate in predicting ambulation independence in patients with stroke during the acute phase.
Effect of fluidised dried yeast (Saccharomyces cerevisiae)
supplementation on milk composition, somatic cell count and milk
yield at different lactation stages in Polish Holstein-Friesian cows

The nutrition of modern dairy cows is a crucial factor affecting milk yield, its parameters and production economics. Nutritional supplementation is often necessary to ensure that cows receive all the required proteins in their diet. The aim of the study was to analyse the impact of fluidised dried yeast ( Saccharomyces cerevisiae ) on daily milk yield, milk yield for all lactation stages, and udder condition. Milk samples were collected before the experiment, during a 4-week period of yeast supplementation, and 4 weeks after the experiment to analyse changes in milk composition and yield. The results demonstrated a significant positive effect ( P < 0.01) on daily milk yield at all stages of lactation, as well as improved udder condition, as evidenced by lower somatic cell counts in milk. Therefore, the results have confirmed that fluidised dried yeast can be a valuable component of the diet for high-yielding dairy cows. However, further analyses are necessary to determine the long-term influence of yeast supplementation on milk production and the overall health of cows.
Assessing the risk of Fusarium oxysporum f. sp. cubense Tropical Race 4 outbreaks in Ecuadorian banana crops using spatial climatic data

The Musaceae family is susceptible to Fusarium wilt (Fw), which is considered the most important disease globally, caused by a group of Fusarium species that includes F. oxysporum f. sp. cubense tropical race 4 (FocTR4). Until recently, FocTR4 was not present in Latin America. However, wilting, chlorosis of leaves, and vascular discoloration (typical symptoms of Fw) were observed in at least a hundred Cavendish plants located in Colombia, Peru and Venezuela in 2019, 2021 and 2022, respectively. Normally, the disease is more severe throughout the warmer and rainy months of the year. Since Ecuador is the world's leading exporter of bananas, including plantains, this study aimed to identify agroclimatic favorability zones for FocTR4 potential incidence in the country, testing linear models to evaluate disease occurrence in relation to climatic conditions and map favorability zones. Most of the banana-producing provinces, including Guayas, Los Ríos, El Oro, Manabí, Santa Elena, and Esmeraldas, presented an estimate ranging from medium-low to very high. In Guayas and Los Rios, the agroclimatic favorability zones of the main Ecuadorian producer provinces for a very high-risk account for almost 50%. This information can help make preventive management decisions in zones with a greater risk of spreading FocTR4.
Extra Virgin Olive Oil-Based Formulations: A “Green” Strategy against Chlamydia trachomatis

In recent decades, antibiotic misuse has emerged as an important risk factor for the appearance of multi-drug-resistant bacteria, and, recently, antimicrobial resistance has also been described in Chlamydia trachomatis as the leading cause of bacterial sexually transmitted diseases worldwide. Herein, we investigated, for the first time, the antibacterial activity against C. trachomatis of a polyphenolic extract of extra virgin olive oil (EVOO), alongside purified oleocanthal and oleacein, two of its main components, in natural deep eutectic solvent (NaDES), a biocompatible solvent. The anti-chlamydial activity of olive-oil polyphenols (OOPs) was tested in the different phases of chlamydial developmental cycle by using an in vitro infection model. Transmission and scanning electron microscopy analysis were performed for investigating potential alterations of adhesion and invasion, as well as morphology, of chlamydial elementary bodies (EBs) to host cells. The main result of our study is the anti-bacterial activity of OOPs towards C. trachomatis EBs down to a total polyphenol concentration of 1.7 μg/mL, as shown by a statistically significant decrease (93.53%) of the total number of chlamydial-inclusion-forming units (p < 0.0001). Transmission and scanning electron microscopy analysis supported its anti-chlamydial effect, suggesting that OOP might damage the chlamydial outer layers, impairing their structural integrity and hindering EB capability to infect the host cell. In conclusion, OOPs may represent an interesting alternative therapeutic option toward C. trachomatis, although further studies are necessary for exploring its clinical applications.
A Novel Method of Moments for Numerical Analysis of Antennas Over 2-D Infinite Periodic Arrays of Scatterers

In this article, a novel method of moments (MoM) for numerical analysis of antennas over a 2-D infinite periodic array of scatterers is proposed. The proposed MoM models the 2-D infinite periodic array of scatterers as a reflecting plane, i.e., electromagnetic response of the 2-D infinite periodic array of scatterers is formulated via their reflection coefficient. In a similar manner to a layered media Green’s function, self/mutual coupling between source and observation points over the 2-D infinite periodic array of scatterers is formulated as a superposition of direct wave component and TE/TM reflection wave components. Numerical simulation is performed, and performance of the proposed MoM is demonstrated. The proposed MoM has a couple of advantages. The first and second ones are mesh-free/numerical modelings of the 2-D infinite periodic array of scatterers via their reflection coefficient. The mesh-free modeling contributes to small computational cost whereas the numerical modeling enables to deal with the 2-D infinite periodic array of arbitrary-shaped scatterers. The third one is ease of combination with existent numerical analysis tool of the 2-D infinite periodic array of scatterers.