Randomized And Parallel Algorithms For Distance Matrix Calculations In Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a vital problem in biology. Optimal alignment of multiple sequences becomes impractical even for a modest number of sequences [1] since the general version of the problem is NP-hard. Because of the high time complexity of traditional MSA algorithms, even today's fast computers are not able to solve the problem for large number of sequences. In this paper we present a randomized algorithm to calculate distance matrices, which is a major step in many multiple sequence alignment algorithms. The basic idea employed is sampling (along the lines of [2]). We also illustrate how to parallelize this algorithm. In Section 1 we introduce the problem of multiple sequence alignments. In Section 2 we provide a discussion on various methods that have been employed in the literature for Multiple Sequence Alignment. In this section we also introduce our new sampling approach. We extend our randomized algorithm to the case of non-uniform length sequences as well. We show that our algorithms are amenable to parallelism in Section 3. In Section 4 we back up our claim of speedup and accuracy with empirical data and examples. In Section 5 we provide some concluding remarks.     

Efficacy of various concentrations of NaOCl and instrumentation techniques in reducing Enterococcus faecalis within root canals and dentinal tubules

AIM: To evaluate the efficacy of 0.5%, 2.5% and 5.25% sodium hypochlorite (NaOCl) as intracanal irrigants associated with hand and rotary instrumentation techniques against Enterococcus faecalis within root canals and dentinal tubules. METHODOLOGY: A total of 180 extracted human premolar teeth were infected for 21 days with E. faecalis. The specimens were divided into 12 groups, as follows: group 1: 5.25% NaOCl + Hybrid technique (Valdrighi et al. 1998); group 2: 5.25% NaOCl + nickel-titanium (NiTi) rotary technique 4 mm shorter than the apex (by FOP-UNICAMP); group 3: 5, 25% NaOCl + NiTi rotary technique (Hero 642); group 4: 2.5% NaOCl +Hybrid technique; group 5: 2.5% NaOCl + NiTi rotary technique 4 mm shorter than the apex; group 6: 2.5% NaOCl + NiTi rotary technique (Hero 642); group 7: 0.5% NaOCl + Hybrid technique; group 8: 0.5% NaOCl + NiTi rotary technique 4 mm shorter than the apex; group 9: 0.5% NaOCl + NiTi rotary technique (Hero 642); group 10: sterile saline solution + Hybrid technique; group 11: sterile saline solution + NiTi rotary technique 4 mm shorter than the apex; group 12: sterile saline solution + NiTi rotary technique (Hero 642). Canals were sampled before and after preparation. After serial dilution, samples were plated onto brain heart infusion (BHI) agar, and the colony forming units (CFU) that were grown were counted. The teeth were sectioned into three thirds and dentine chips were removed from the canals with conical burs. The samples obtained with each bur were immediately collected into test tubes containing BHI broth, and were incubated at 37 degrees C and plated onto BHI agar. The CFU were counted and analysed. RESULTS: At all depths and thirds of the root canals and for all techniques used, 5.25% NaOCl was shown to be the most effective irrigant solution tested when dentinal tubules were analysed, followed by 2.5% NaOCl. No differences among concentrations in cleaning the canals were found. CONCLUSIONS: Especially at higher concentrations, NaOCl, was able to disinfect the dentinal tubules, independent of the canal preparation technique used.     

KIR2DS2 and KIR2DS4 promoter hypomethylation patterns in patients undergoing hematopoietic cell transplantation (HCT)

The killer cell Ig-like receptor (KIR)–MHC class I pathway is an integral part of natural killer cell immunity, and its role in host protection from both cancer and infection is important. In addition, we have shown elevated KIR2DS2 and 2DS4 expression in PBMCs of patients undergoing hematopoietic cell transplantation (HCT) [1]. Since all inhibitory KIR promoters are known to be heavily methylated, the question asked here is how and when KIR2DS2 and 2DS4 promoters had changed their methylation profile in association with HCT.     

Burn depth assessment by dual-wavelength light emitting diodes-excited photoacoustic imaging in rats

Accurate burn depth assessment is crucial to determine treatment plans for burn patients. We have previously proposed a method for performing burn depth assessments based on photoacoustic (PA) imaging, and we have demonstrated the validity of this method, which allows the successful detection of PA signals originating from the blood under the bloodless burned tissue, using rat burn models. Based on these findings, we started a clinical study in which we faced two technical issues: (1) When the burn depth was shallow, PA signals due to skin contamination and/or melanin in the epidermis (surface signals) could not be distinguished from PA signals originating from the blood in the dermis; (2) the size of the system was too large. To solve these issues, we propose a burn depth diagnosis based on dual-wavelength light emitting diodes (LEDs)-excited PA imaging. The use of LEDs rendered the system compact compared to the previous one that used a conventional solid-state laser. We replicated human burned skin by applying a titrated synthetic melanin solution onto the wound surface in albino rat burn models and measured their burn depths by PA excitation at 690 and 850 nm, where melanin and haemoglobin show greatly different absorption coefficients. As a result, the surface signals were eliminated by subtracting the PA signals at 690 nm from those at 850 nm. The resultant estimated burn depths were strongly correlated with the histological assessment results. The validity of the proposed method was also examined using a burn model of rats with real melanin.     

A challenge of deep-learning-based object detection for hair follicle dataset

Background

Deep-learning object detection has been applied in various industries, including healthcare, to address hair loss.

Methods

In this paper, YOLOv5 object detection algorithm was used to detect hair follicles in a small and specific image dataset collected using a specialized camera on the scalp of individuals with different ages, regions, and genders. The performance of YOLOv5 was compared with other popular object detection models.

Results

YOLOv5 performed well in the detection of hair follicles, and the follicles were classified into five classes based on the number of hairs and the type of hair contained. In single-class object detection experiments, a smaller batch size and the smallest YOLOv5s model achieved the best results, with an map of 0.8151. In multiclass object detection experiments, the larger YOLOv5l model was able to achieve the best results, and batch size affected the result of model training.

Conclusion

YOLOv5 is a promising algorithm for detecting hair follicles in a small and specific image dataset, and its performance is comparable to other popular object detection models. However, the challenges of small-scale data and sample imbalance need to be addressed to improve the performance of target detection algorithms.     

Handheld microfocused ultrasound device for facial lifting: A preliminary study of ULTIGHT

Objective

Although focused ultrasound modalities have achieved positive clinical results in noninvasive skin rejuvenation, they presented various side effects and particularly severe pain during treatment. This study introduces a microfocused ultrasound (MFU) device, ULTIGHT, to overcome the severe pain issue, providing quasi-facial lifting.

Materials and Methods

Transducer surface was imaged with a scanning electron microscope. The energies of four treatment cartridges were measured using an ultrasound power meter. In vitro experiments were performed to quantitatively evaluate the MFU thermal zones (MFUTZs) and treatment line (TL) of 10 MFUTZs. Ex vivo experiments were performed to evaluate the MFUTZs and temperature rise in tissue. Clinical trials using eight volunteers were performed to qualitatively evaluate facial lifting.

Results

The MFU transducer clearly showed a smooth and no air gap surface. ULTIGHT produced 10 discrete MFUTZs in a TL of length 10 mm. In ex vivo tissue, discrete linear MFUTZs were clearly observed at lower number of TLs; however, they started to aggregate at higher number of TLs. The temperature rise was linearly increased as a function of the number of treatments. A single MFUTZ resulted in a temperature rise of 3°C–10°C that could cause hyperthermia for body temperature. In the clinical trials, the volunteers showed quasi-facial lifting right after treatment on the lower facial region.

Conclusions

ULTIGHT provides relatively low energy, which may be advantageous or disadvantageous depending on clinical applications. Additionally, it has the advantage of being pain-free even without anesthetic during treatment, providing quasi-facial lifting right after treatment.