Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Barcoding: Error Rates Based on Comprehensive Sampling

DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a “barcoding gap” between the two, we find substantial overlap, leading to minimal error rates of ~17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.
Recent Trends in S. aureus and E. coli-Based Endometritis, and the Therapeutic Evaluation of Sodium Alginate-Based Antibiotics and Nanoparticles

Postpartum infection of the uterus by pathogenic bacteria is exacerbated due to a lack of sufficient epidemiological studies and evidence-based therapeutics. Therefore, this study was planned to find the prevalence, risk factors, and drug-resistance profile of S. aureus and E. coli isolated from bovine endometritis and to evaluate the antibacterial potential of sodium alginate-based antibiotics and nanoparticles. The study revealed 34.21% S. aureus and 31.57% E. coli, whereas most of the assumed risk factors presented significant association in this study. S. aureus showed the highest resistance against fusidic acid (60%) and cefoxitin (50%), while the highest resistance in E. coli was found against fusidic acid (60%), gentamicin (60%), chloramphenicol (50%), and cefoxitin (50%). Tylosin coupled with MgO nanoparticles stabilized in sodium alginate gel (Tylo + MgO + gel) presented significantly lower minimum inhibitory concentration (MIC) against E. coli, showing 13.88 ± 4.51 µg/mL after 24 h incubation. On the other hand, gel-based preparations showed MIC as 31.25 ± 0 µg/mL (Tylo + gel + MgO) and 26.04 ± 9.02 µg/mL (Tylo + Gel) against S. aureus. Generally, the MICs of non-gel-based preparations were significantly higher against bacteria except ampicillin against S. aureus in this study. The toxicity analysis of MgO nanoparticles presented 20–80% mortality of snails against a wider range of 0.01 mg/mL–10 mg/mL. The histopathological parameters concluded MgO nanoparticles safe to use on off targets. The current study thus concludes the rise in antimicrobial resistance while the gel-based products appearing as effective antimicrobials with sufficient safety margins for off-targets. The study thus invites further investigation for the development of suitable and affordable modified therapeutics for better health and production of animals.
Lightweight colon polyp segmentation algorithm based on improved DeepLabV3+

To address the problems that the current polyp segmentation model is complicated and the segmentation accuracy needs to be further improved, a lightweight polyp segmentation network model Li-DeepLabV3+ is proposed. Firstly, the optimized MobileNetV2 network is used as the backbone network to reduce the model complexity. Secondly, an improved simple pyramid pooling module is used to replace the original Atrous Spatial Pyramid Pooling structure, which improves the model training efficiency of the model while reducing the model parameters. Finally, to enhance the feature representation, in the feature fusion module, the low-level feature and the high-level feature are fused using the improved Unified Attention Fusion Module, which applies both channel and spatial attention to enrich the fused features, thus obtaining more boundary information. The model was combined with transfer learning for training and validation on the CVC-ClinicDB and Kvasir SEG datasets, and the generalization of the model was verified across the datasets. The experiment results show that the Li-DeepLabV3+ model has superior advantages in segmentation accuracy and segmentation speed, and has certain generalization abilities.
The relative importance of calving and surface ablation at a lacustrine terminating glacier : a detailed assessment of ice loss at Bridge Glacier, British Columbia

Bridge Glacier is a lacustrine calving glacier located in the southern Coast Mountains and terminates in a 6.2 km2 proglacial lake. The glacier has retreated more than 3.55 km up-valley since 1984, the majority of the retreat having occurred since 2003. While surface melt may have contributed to the retreat, calving allowed for an additional annual volume of ice loss. The relative contributions from surface melt and calving to the total volume of ice loss is examined for the 2013 melt season. Surface melt is quantified using on-glacier meteorological data to drive a distributed energy balance model. The calving flux is quantified using field measurements of lake bathymetry, terminus area change, and ice thickness. Calving flux estimates are completed by daily measurements of terminus surface velocity derived from manual feature tracking using oblique time lapse camera imagery. Calving accounts for 23% of the total ice loss in the 2013 melt season, suggesting that surface melt is the main driver of mass loss at Bridge Glacier. Data from the 2013 field season is used to inform historical calving flux and surface melt estimates from 1984 to 2013. The calving flux is minor until 1991, at which point the glacier terminus achieves flotation, and begins to discharge large tabular icebergs. Calving was characterized by large, multi-annual retreats, alternating with periods of relative stability. The calving flux peaked from 2005 to 2010, when it was roughly equal to the mass loss due to surface melt. Calving was a much smaller contributor of mass loss from Bridge Glacier, except for a transient high-calving period in the late 2000s. Looking forward, Bridge Glacier will retreat into shallower water where the terminus will no longer float, and calving losses should decrease substantially. Although calving losses will become an increasingly minor portion of the mass balance, future retreat is expected at Bridge Glacier due to a legacy of dynamic thinning brought about by its transient calving phase.
Preparation and Characterization of Graphene

The homogeneous-dispersed graphene oxide was prepared by the improved Hummers method, which would be reduced to graphene with the reducing agent called hydrazine hydrate. The X-ray diffraction, Infrared spectroscopy, Raman spectra and Transmission electron microscopy were used to analysis the phase, morphology and structure of the graphene and graphene oxide. The results show that the graphene oxide and reduced graphene oxide prepared via this method, whose degree of oxidation and reduction are high; Also obtained a higher well-disperses and less structural imperfection of the graphene that was manufactured in the reducing system that added ammonia reduction
DNA Methylation of the IL-17A Gene Promoter Is Associated with Subclinical Atherosclerosis and Coronary Artery Disease: The Genetics of Atherosclerotic Disease Mexican Study

The interleukin-17 (IL-17) has a crucial role during inflammation and has been associated with cardiovascular diseases, but its role in epigenetics is still poorly understood. Therefore, the aim of this study was to evaluate the DNA methylation status of the IL-17A gene promoter to establish whether it may represent a risk factor for subclinical atherosclerosis (SA) or clinical coronary artery disease (CAD). We included 38 patients with premature CAD (pCAD), 48 individuals with SA, and 43 healthy controls. Methylation in the CpG region of the IL-17A gene promoter was assessed via methylation-specific polymerase chain reaction (MSP). Individuals with SA showed increased methylation levels compared to healthy controls and pCAD patients, with p < 0.001 for both. Logistic regression analysis showed that high methylation levels represent a significant risk for SA (OR = 5.68, 95% CI = 2.38–14.03, p < 0.001). Moreover, low methylation levels of the IL-17A gene promoter DNA represent a risk for symptomatic pCAD when compared with SA patients (OR = 0.16, 95% CI = 0.06–0.41, p < 0.001). Our data suggest that the increased DNA methylation of the IL-17A gene promoter is a risk factor for SA but may be a protection factor for progression from SA to symptomatic CAD.
A guide to restoring inanga habitat

5 Introduction 5 Inanga stream habitat 7 Location and physical attributes 7 Access 9 Cover 12 Water quality 16 Water temperature 16 pH 16 Ammonia 16 Dissolved oxygen 17 Suspended sediment 17 Other pollutants 17 Inanga stream management and enhancement 18 Inanga spawning habitat 20 Locating spawning sites 20 Equipment 21 High tide searches 21 Low tide searches 21 When, where, and what to look for 22 When 22 Where 22 What to look for 24 Spawning site management and enhancement 25 Summary 26 Acknowledgments 27 References 27 Appendix 1 31
Impact of Hypoxia-Induced miR-210 on Pancreatic Cancer

Pancreatic cancer (PC) poses significant clinical challenges, with late-stage diagnosis and limited therapeutic options contributing to its dismal prognosis. A hallmark feature of PC is the presence of a profoundly hypoxic tumour microenvironment, resulting from various factors such as fibrotic stroma, rapid tumour cell proliferation, and poor vascularization. Hypoxia plays a crucial role in promoting aggressive cancer behaviour, therapeutic resistance, and immunosuppression. Previous studies have explored the molecular mechanisms behind hypoxia-induced changes in PC, focusing on the role of hypoxia-inducible factors (HIFs). Among the myriad of molecules affected by hypoxia, microRNA-210 (miR-210) emerges as a central player. It is highly responsive to hypoxia and regulated by HIF-dependent and HIF-independent pathways. miR-210 influences critical cellular processes, including angiogenesis, metastasis, and apoptosis, all of which contribute to PC progression and resistance to treatment. Understanding these pathways provides insights into potential therapeutic targets. Furthermore, investigating the role of miR-210 and its regulation in hypoxia sheds light on the potential development of early diagnostic strategies, which are urgently needed to improve outcomes for PC patients. This review delves into the complexities of PC and introduces the roles of hypoxia and miR-210 in the progression of PC.
Magnesium: Effect on ocular health as a calcium channel antagonist Magnezyum: Kalsiyum kanal antagonisti olarak göz sağliği üzerindeki etkileri

Magnesium is the physiologic calcium channel blocker, involving in many different metabolic processes by maintaining cell membrane function, modulating smooth muscle contraction and influencing enzymatic activities. Mag nesium has been shown to increase blood flow to tissues by modifying endothelial function via endothelin-1 (ET-1) and nitric Oxide (NO) pathways. Magnesium also exhibits neuroprotective role by blocking N-methyl-D-aspartate (NMDA) receptor related calcium influx and by inhibiting the release of glutamate, hence protects the cell against oxidative stress and apoptosis. Both increase in blood flow and its neuroprotective effect make magnesium a good candidate for glaucoma studies. Magnesium has been shown to decrease oxidative stress and apoptosis in retinal tissue and to have retinal ganglion cell sparing effect. A series of studies has been conducted about magnesium could decrease insulin resistance in diabetic patients, ease glycemia control and prevent diabetic retinopathy. Magnesium is found to be critically important in maintaining normal ionic homeostasis of lens. Magnesium deficiency has been shown to cause increased lenticular oxidative stress and ionic imbalance in the lens so trigger cataractogenesis. J Clin Exp Invest 2013; 4 (2): 244-251
An introduction to rggobi

The rggobi package provides a command-line interface to GGobi, an interactive and dynamic graphics package. Rggobi complements GGobi’s graphical user interface, providing a way to fluidly transition between analysis and exploration, as well as automating common tasks. It builds on the first version of rggobi to provide a more robust and user friendly interface. In this article, we will show you how you can starting using rggobi now, and learn some ways to gain insight into your data using a combination of analysis and visualisation. We do assume some familiarity with GGobi. If you’re not familiar, but would like to learn more have a look at the GGobi web site, http://www. ggobi.org, especially the demos of GGobi’s capabilities found at http://www.ggobi.org/docs. You will also need to have a copy of GGobi installed before continuing: download a version for your platform from http://www.ggobi.org/downloads. You can then install rggobi and it’s dependencies using install.packages("rggobi", dep=T). This article introduces the three main components of rggobi, with examples of how youmight use them in day-to-day tasks:
KICO: Surgeon-Centered Collaborative Tool to Aid Peritoneal Carcinomatosis Assessment

Peritoneal carcinomatosis is a major concern in gastric and colorectal cancers where assessments of the peritoneum are crucial for prognosis. This work proposes KICO, a surgeon-centered collaborative tool to aid peritoneal nodules detection and laparoscopic videos analysis. Surgeons’ specificity on software requirements made off-the-shelf marking tools unfit, especially to capture high-quality data. When catering to the surgeons’ need, the design process of the system relied on user-centered design and a tool for collaboration. KICO aims to aid surgeons annotate areas of interest during examination and provide standardized examination reports which include the Peritoneal Carcinomatosis Index score. Implementation of the system uses an Angular front-end with a service-oriented Go back-end which is executed within Docker containers. System evaluation was done by analyzing system usability with System Usability Scale and capturing the system’s level of usage. This work concludes that KICO successfully aided surgeons on creating reports on peritoneal carcinomatosis assessments on laparoscopic surgeries with high usability score and saw exceptional frequency of use.
PianoSyncAR: Enhancing Piano Learning through Visualizing Synchronized Hand Pose Discrepancies in Augmented Reality

Motor skill acquisition involves learning from spatiotemporal discrepancies between target and self-generated motions. However, in dexterous skills with numerous degrees of freedom, understanding and correcting these motor errors are challenging. This issue becomes crucial for experienced individuals who seek for mastering and sophisticating their skills, where even subtle errors need to be minimized. To enable efficient optimization of body posture in piano learning, we present PianoSyncAR, an augmented reality system that superimposes the time-varying complex hand postures of a teacher over the hand of a learner. Through a user study with 12 pianists, we demonstrate several advantages of the proposed system over conventional tablet-screen, which implicate the potential of AR training as a complementary tool for video-based skill learning in piano playing.
Estimating the 3D center point of an object with Kinect sensor RGB-D images

This article describes the estimation of a 3D point using a Kinect sensor and the Robot Operating System (ROS) along with You Only Look Once (YOLO) for object detection. The Kinect sensor provides RGB-D images, which are used to create a Point Cloud representing the geometry of the environment. ROS is used as a robotics development framework, while YOLO is employed to identify objects in the scene. The article presents the packages used, the datasets used for measurement, and the configuration of ROS and YOLO. Additionally, the functionalities of RViz, a 3D visualization tool used in the tests, are explored. Furthermore, it covers the methods employed, the acquired data, and an analysis of the error margin in relation to the measurement of the distance between the Kinect and the object. The findings and techniques presented in this study contribute to addressing the challenges faced in the RoboCup@Home competition, specifically in the context of object manipulation tasks.
The effect of grain size on thermal conductivity of quartz sands and silts

Synthetic samples of different grain size fractions of quartz were prepared and the thermal conductivities measured with a divided bar apparatus. The measurements were carried out on dried and water-saturated samples both perpendicular and parallel to the main stress direction during compaction of the samples. A clear correlation was observed between the porosity and the measured thermal conductivities. For water-saturated samples the thermal conductivity decreases more with increasing porosity than for ideal isotropic material as predicted by the geometric mean model. A clear positive correlation was also found between the thermal conductivity and the grain sizes of the samples. When the expected effect of porosity on the thermal conductivity was excluded, a linear correlation between the logarithm of the grain size and the measured thermal conductivities of the water-saturated samples was found. An anisotropy effect (a = k/k 1 ) in thermal conductivity was observed for the samples, being most prominent for the coarsest ones. The measured anisotropy is assumed to be mainly due to the thermal anisotropic nature of the quartz crystal.
A retrospective study of glucose homeostasis, insulin secretion, sensitivity/resistance in non- transfusion-dependent β-thalassemia patients (NTD- β Thal): reduced β-cell secretion rather than insulin resistance seems to be the dominant defect for glucose dysregulation (GD)

Aims: Non-transfusion - dependent β-thalassemias (NTD-βThal) can cause iron overload and serious iron-related organ complications as endocrine dysfunction, including glucose dysregulation (GD). Patients and methods: We retrieved data of all NTD- β Thal patients referred consecutively to a single Outpatient Italian Clinic from October 2010 to April 2023. All patients underwent a standard 3-h oral glucose tolerance test (OGTT) for analysis of glucose homeostasis, insulin secretion and sensitivity/resistance (IR), using conventional surrogate indices derived from the OGTT. The collected data in NTD- β Thal patients were compared to 20 healthy subjects. Results: Seventeen of 26 (65.3 %) NTD- β Thal patients (aged: 7.8 -35.1 years) had normal glucose tolerance, 1/26 (3.8 %) had impaired fasting glucose (IFG), 5/26 (19.2 %) impaired glucose tolerance (IGT), 1/26 (3.8%) IFG plus IGT and 2/26 (7.6%) plasma glucose (PG) level ≥155 mg/dL 1-h after glucose load. GD was observed exclusively in young adult patients; none of them had diabetes mellitus (DM). These findings were associated with a low insulinogenic index (IGI) and oral disposition index. HOMA-IR and QUICKI were not significantly different compared to controls. Interestingly, in young adult patients, ISI-Matsuda index was statistically higher compared to the control group, suggesting an increased insulin sensitivity. Conclusions: This study reported a high prevalence of GD in young adults with NTD- β Thal. The documented reduction of IGI rather than the presence of IR, indicates reduced insulin secretory capacity as the pathophysiological basis of dysglycemia that may represent a novel investigational path for future studies on the mechanism(s) responsible for GD in NTD- β Thal patients. (www.actabiomedica.it)
Study on calculation for shield tunneling-induced ground movements in clays

The extent of soil disturbance induced by shield tunneling construction is analyzed.It is considered that the assumed boundary condition of ground loss in Loganathan’s formula exists error based on the principle of limit equilibrium.The influence of internal friction angle on ground movements is taken into account.It is considered that the level obliquity about boundary line of the vertical ground formation region should be(45°+? /2),but not 45°. The modified Loganathan’s formula is presented,which is only applicable under the undrained condition in clays.At the same time,the calculation for the extent of the cut disturbance of shield is advanced for the first time.As shown by analytical calculation for a project case,the proposed new approach tends to decrease the width of surface settlement troughs and horizontal ground displacements;and the results are more accordant with the field observations when compared with results of Loganathan’s formula.
Early Blood Clot Detection Using Forward Scattering Light Measurements Is Not Superior to Delta Pressure Measurements

The occurrence of thrombus formation within an extracorporeal membrane oxygenator is a common complication during extracorporeal membrane oxygenation therapy and can rapidly result in a life-threatening situation due to arterial thromboembolism, causing stroke, pulmonary embolism, and limb ischemia in the patient. The standard clinical practice is to monitor the pressure at the inlet and outlet of oxygenators, indicating fulminant, obstructive clot formation indicated by an increasing pressure difference (ΔP). However, smaller blood clots at early stages are not detectable. Therefore, there is an unmet need for sensors that can detect blood clots at an early stage to minimize the associated thromboembolic risks for patients. This study aimed to evaluate if forward scattered light (FSL) measurements can be used for early blood clot detection and if it is superior to the current clinical gold standard (pressure measurements). A miniaturized in vitro test circuit, including a custom-made test chamber, was used. Heparinized human whole blood was circulated through the test circuit until clot formation occurred. Four LEDs and four photodiodes were placed along the sidewall of the test chamber in different positions for FSL measurements. The pressure monitor was connected to the inlet and the outlet to detect changes in ΔP across the test chamber. Despite several modifications in the LED positions on the test chamber, the FSL measurements could not reliably detect a blood clot within the in vitro test circuit, although the pressure measurements used as the current clinical gold standard detected fulminant clot formation in 11 independent experiments.
The Prototype of the Eight-element Antenna Array for V2I Communication Systems

The paper presents the results of designing an emitter and a linear eight-element antenna array for intelligent transport systems (ITS) applications and the Vehicle-to-Infrastructure (V2I) technology. The operating band of the emitter contains the range allocated in the Russian Federation for telematic devices in transport 5725–5875 MHz. Based on the emitter simulation model, the prototype was fabricated using the Arlon AD 255C substrate with a dielectric constant of 2.55. Further, a linear eight-element antenna array with dimensions of 303.3 x 45.5 mm was assembled from emitter prototypes. The antenna array prototype achieves resonance at 5875 MHz and performs an operating band of 275 MHz. The fabricated prototypes were also measured in an anechoic chamber. The antenna array radiation pattern demonstrates the main lobe is 8 degrees wide at FWHM, and the side lobes level does not exceed -10 dB.