Miracle-dz/UniFAR-FTUs huggingface dataset:
DAPnet: A Double Self-Attention Convolutional Network for Point Cloud Semantic Labeling

Airborne laser scanning (ALS) point clouds have complex structures, and their 3D semantic labeling has been a challenging task. It has three problems: 1) The difficulty of classifying point clouds around boundaries of objects from different classes, 2) the diversity of shapes within the same class, and 3) the scale differences between classes. In this study, we propose a novel double self-attention convolutional network called the DAPnet. The double self-attention includes the point attention module (PAM) and the group attention module (GAM). For problem 1), the PAM can effectively assign different weights based on the relevance of point clouds in adjacent areas. Meanwhile, for problem 2), the GAM enhances the correlation between groups, i.e., grouped features within the same classes. To solve problem 3), we adopt a multiscale radius to construct the groups and concatenate extracted hierarchical features with the output of the corresponding upsampling process. Under the ISPRS 3D Semantic Labeling Contest dataset, the DAPnet outperforms the benchmark by 85.2% with an overall accuracy of 90.7%. By conducting ablation comparisons, we find that the PAM effectively improves the model than the GAM. The incorporation of the double self-attention module has an average of 7% improvement on the pre-class accuracy. Plus, the DAPnet consumes a similar training time to those without the attention modules for model convergence. The DAPnet can assign different weights to features based on the relevance between point clouds and their neighbors, which effectively improves classification performance.
New Encoder Learning for Captioning Heavy Rain Images via Semantic Visual Feature Matching

Image captioning generates text that describes scenes from input images. It has been developed for high-quality images taken in clear weather. However, in bad weather conditions, such as heavy rain, snow, and dense fog, poor visibility as a result of rain streaks, rain accumulation, and snowflakes causes a serious degradation of image quality. This hinders the extraction of useful visual features and results in deteriorated image captioning performance. To address practical issues, this study introduces a new encoder for captioning heavy rain images. The central idea is to transform output features extracted from heavy rain input images into semantic visual features associated with words and sentence context. To achieve this, a target encoder is initially trained in an encoder–decoder framework to associate visual features with semantic words. Subsequently, the objects in a heavy rain image are rendered visible by using an initial reconstruction subnetwork (IRS) based on a heavy rain model. The IRS is then combined with another semantic visual feature matching subnetwork (SVFMS) to match the output features of the IRS with the semantic visual features of the pretrained target encoder. The proposed encoder is based on the joint learning of the IRS and SVFMS. It is trained in an end-to-end manner, and then connected to the pretrained decoder for image captioning. It is experimentally demonstrated that the proposed encoder can generate semantic visual features associated with words even from heavy rain images, thereby increasing the accuracy of the generated captions.
Spike Protein NTD mutation G142D in SARS-CoV-2 Delta VOC lineages is associated with frequent back mutations, increased viral loads, and immune evasion

The significantly greater infectivity of the SARS-CoV-2 Delta variants of concern (VOC) is hypothesized to be driven by key mutations that result in increased transmissibility, viral load and/or evasion of host immune response. We surveyed the mutational profiles of Delta VOC genomes between September 2020 and mid-August 2021 and identified a previously unreported mutation pattern at amino acid position 142 in the N-terminal domain (NTD) of the spike protein which demonstrated multiple rounds of mutation from G142 to D142 and back. This pattern of frequent back mutations was observed at multiple time points and across Delta VOC sub-lineages. The etiology for these recurrent mutations is unclear but raises the possibility of host-directed editing of the SARS-CoV-2 genome. Within Delta VOC this mutation is associated with higher viral load, further enhanced in the presence of another NTD mutation (T95I) which was also frequently observed in these cases. Protein modeling of both mutations predicts alterations of the surface topography of the NTD by G142D, specifically disturbance of the 'super site' epitope that binds NTD-directed neutralizing antibodies (NAbs). The appearance of frequent and repeated G142D followed by D142G back mutations is previously unreported in SARS-CoV-2 and may represent viral adaptation to evolving host immunity characterized by increasing frequency of spike NAbs, from both prior infection and vaccine-based immunity. The emergence of alterations of the NTD in and around the main NAb epitope is a concerning development in the ongoing evolution of SARS-CoV-2 which may contribute to increased infectivity, immune evasion and 'breakthrough infections' characteristic of Delta VOC. Future vaccine and therapy development may benefit by recognizing the emergence of these novel spike NTD mutations and considering their impact on antibody recognition, viral neutralization, infectivity, replication, and viral load.
Recent developments in antifungal lactic acid bacteria: Application, screening methods, separation, purification of antifungal compounds and antifungal mechanisms

Abstract Fungal contamination of food, which causes large economic losses and public health problems, is a global concern. Chemical methods are typically used in the food industry to inhibit the growth of spoilage fungus, but there are several drawbacks of chemical methods. Thus, the development of consumer-friendly and ecologically sustainable biological preservation technology has become a hot spot in food research. As a natural biological control agent, lactic acid bacteria (LAB) is a good choice in food preservation due to its antifungal properties. In order to screen and identify new antifungal LAB and antifungal compounds, this review compares three screening methods (overlay method, agar diffusion method, and microplate inhibition method) of antifungal LAB and summarizes the separation and purification techniques of antifungal compounds. A discussion of the effects of LAB, media, temperature, pH, and incubation period on the antifungal activity of LAB to highlight the antifungal properties of LAB for future studies then follows. Additionally, the antifungal mechanism of LAB is elucidated from three aspects: 1) LAB cells, 2) antifungal compounds, and 3) co-cultivation. Finally, research regarding antifungal LAB in food preservation (fruits, vegetables, grain cereals, bakery products, and dairy products) is summarized, which demonstrates the potential application value of LAB in food.
Mammography-based radiomics for predicting the risk of breast cancer recurrence: a multicenter study.

OBJECTIVE This study aimed to establish a mammography-based radiomics model for predicting the risk of estrogen receptor (ER)-positive, lymph node (LN)-negative invasive breast cancer recurrence based on Oncotype DX and validated it by using multicenter data. METHODS A total of 304 potentially eligible patients with pre-operative mammography images and available Oncotype DX score were retrospectively enrolled from two hospitals. The patients were grouped as training set (168 patients), internal test set (72 patients), and external test set (64 patients). Radiomics features were extracted from the mammography images of each patient. Spearman correlation analysis, analysis of variance, and least absolute shrinkage and selection operator regression were performed to reduce the redundant features in the training set, and the least absolute shrinkage and selection operator algorithm was used to construct the radiomics signature based on selected features. Multivariate logistic regression was utilized to construct classification models that included radiomics signature and clinical risk factors to predict low vs intermediate and high recurrence risk of ER-positive, LN-negative invasive breast cancer in the training set. The models were evaluated with the receiver operating characteristic curve in the training set. The internal and external test sets were used to confirm the discriminatory power of the models. The clinical usefulness was evaluated by using decision curve analysis. RESULTS The radiomics signature consisting of three radiomics features achieved favorable prediction performance. The multivariate logistic regression model including radiomics signature and clinical risk factors (tumor grade and HER 2) showed good performance with areas under the curve of 0.92 (95% confidence interval [CI] 0.86 to 0.97), 0.88 (95% CI 0.75 to 1.00), and 0.84 (95% CI 0.69 to 0.99) in the training, internal and external test sets, respectively. The DCA indicated that when the threshold probability is ranges from 0.1 to 1.0, the radiomics model adds more net benefit than the "treat all" or "treat none" scheme in internal and external test sets. CONCLUSION As a non-invasive pre-operative prediction tool, the mammography-based radiomics model incorporating radiomics and clinical factors show favorable predictive performance for predicting the risk of ER-positive, LN-negative invasive breast cancer recurrence based on Oncotype DX. ADVANCES IN KNOWLEDGE The mammography-based radiomics model incorporating radiomics and clinical factors shows favorable predictive performance for predicting the risk of ER-positive, LN-negative invasive breast cancer recurrence.
A fast, sensitive and cost-effective method for nucleic acid detection using non-radioactive probes

Abstract Nucleic acid detection and quantification using a labeled DNA probe is a very common molecular biology procedure. Here, we describe a new method, based on commonly used laboratory solutions, for nucleic acid hybridization and detection with digoxigenin-labeled DNA probes. The protocol described is faster, more sensitive and much cheaper than a standard protocol using commercial solutions. Comparison with a classical radioactive detection method shows that the latter exhibits less background and shows a greater linear response. Hence, the proposed protocol may be routinely performed for qualitative detection of nucleic acid, but when precise signal quantitation needs to be obtained, radioactive probe hybridization associated to phosphorimaging technology is more reliable.
The ORF45 Protein of Kaposi Sarcoma-Associated Herpesvirus Is an Inhibitor of p53 Signaling during Viral Reactivation

Unlike in other cancers, the tumor suppressor protein p53 is rarely mutated in Kaposi sarcoma (KS). Rather, Kaposi sarcoma-associated herpesvirus (KSHV) inactivates p53 through multiple viral proteins. ABSTRACT Kaposi sarcoma-associated herpesvirus (KSHV) is a carcinogenic double-stranded DNA virus and the etiological agent of Kaposi sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman’s disease (MCD). To prevent premature apoptosis and support its replication cycle, KSHV expresses a series of open reading frames (ORFs) that regulate signaling by the p53 tumor suppressor protein. Here, we describe a novel viral inhibitor of p53 encoded by KSHV ORF45 and identify its mechanism of action. ORF45 binds to p53 and prevents its interactions with USP7, a p53 deubiquitinase. This results in decreased p53 accumulation, localization of p53 to the cytoplasm, and diminished transcriptional activity. IMPORTANCE Unlike in other cancers, the tumor suppressor protein p53 is rarely mutated in Kaposi sarcoma (KS). Rather, Kaposi sarcoma-associated herpesvirus (KSHV) inactivates p53 through multiple viral proteins. One possible therapeutic approach to KS is the activation of p53, which would result in apoptosis and tumor regression. In this regard, it is important to understand all the mechanisms used by KSHV to modulate p53 signaling. This work describes a novel inhibitor of p53 signaling and a potential drug target, ORF45, and identifies the mechanisms of its action.
A double-helix and cross-patterned solenoid used as a wirelessly powered receiver for medical implants

Many medical implants need to be designed in the shape of a cylinder (rod), a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT) direction is from the external power transmission pad (a planar coil) to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH) coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees) to form a cross pattern. The WPT system is designed using the magnetic resonance concept for wireless power transfer (MR-WPT). The power transfer efficiency (PTE) relies on the near-field magnetic coupling which is closely related to the location and orientation of the DH coil. We explain how the novel structure of the DH solenoid magnifies the mutual inductance with the widely adopted circular planner coil and how the PTE is improved in comparison to the case of the conventional solenoid coil. We also study an important case where the double-helix power reception coil is laterally and angularly misaligned with the transmitter. Finally, our computational study using the finite element method and experimental study with actually constructed prototypes are presented which have proven our new double-helix coil design.Many medical implants need to be designed in the shape of a cylinder (rod), a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT) direction is from the external power transmission pad (a planar coil) to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH) coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees) to form a cross pattern. The WPT syst.
Natural menopausal age and cardiovascular disease risk factors in older Chinese women: Guangzhou Biobank Cohort Study

Supplemental Digital Content is available in the text Abstract Objective: To examine the associations of natural menopausal age with cardiovascular disease risk factors and whether the associations varied by parity in older Chinese women. Methods: Information of demographic characteristics, lifestyles, and reproductive factors was collected by face-to-face interview. Framingham Risk Score was used as an indicator of cardiovascular disease risk, with a score ≥ 10% considered as high cardiovascular disease risk (vs low, dichotomous). Multivariable logistic and linear regressions were used to examine the associations of menopausal age with cardiovascular disease risk factors. Results: Of 18,339 women aged 50+ years, the average (standard deviation) age was 61.8 (6.9) years. Compared with women with menopausal age of 45 to 54 years, after adjustment for multiple potential confounders, women with menopausal age <45 years or ≥55 years had higher Framingham Risk Score (0.93%, 95% confidence interval: 0.40-1.46, and 0.69%, 95% confidence interval: 0.18-1.20, respectively). Women with menopausal age <45 or ≥55 years had higher odds of high cardiovascular disease risk (vs low) (odds ratio [95% confidence interval]:1.26 (1.10-1.44) and 1.17 (1.02-1.33), respectively). The associations of menopausal age with the Framingham Risk Score varied by parity (P for interaction ≤0.001). The Framingham Risk Score was higher in those with one to three parity (<45 y: 1.01 [0.43-1.59]; ≥55 y: 1.14 [0.60-1.68]) and lower for parity ≥4 (<45 y: −0.33 [−1.84 to 1.18]; ≥55 y: −2.02 [−3.82 to −0.22]). In nulliparous women, the Framingham Risk Score was highest in menopausal age <45 years (3.97 [1.67-6.26]), but the differences were nonsignificant in menopausal age ≥55 years (0.66 [−1.38 to 2.71]). Conclusions: Both early and late natural menopausal ages were associated with a higher cardiovascular disease risk, and the associations were stronger in those with lower parity. Video Summary:http://links.lww. com/MENO/A813.
Quantitative physical examination indicators to detect patients with stenosis at a high risk of thrombosis at hemodialysis vascular access sites: A retrospective case–control study

Background: Quantitative physical examination (PE) indicators, including palpable pulsatility length and outflow scores, can be used to quantify stenosis severity at hemodialysis vascular access sites. It is known that the risk of high-shear-related thrombosis is increased when the minimal luminal diameter (MLD) of stenosis decreases. At present, MLD is measured using sonography or angiography. This study sought to determine the relationship between quantitative PE indicators and MLD and report their diagnostic performance in detecting patients with stenosis at a high risk of thrombosis. Methods: We performed a retrospective case–control study using routinely collected data. We used the post-stenosis palpable pulsatility length (sPPL) and pulse-and-thrill based outflow score to assess the severity of AVF inflow and outflow stenosis, respectively. We recorded paired quantitative PE indicators and MLD before and after angioplasty in patients enrolled over a 4-month period. Results: A total of 249 paired PE indicators and MLD measurements were obtained from 163 patients. A receiver operating characteristic curve analysis showed that an MLD cutoff value of <1.55 mm and an MLD of <1.95 mm discriminated sPPL = 0 and PESOS (physical examination significant outflow stenosis)/1− of the outflow score, respectively, from all other measurements, with the area under the curve values of 0.8922 and 0.9618, respectively. With sPPL = 0 and PESOS/1− of the outflow score as diagnostic tools to detect inflow stenosis with an MLD of ⩽1.5 mm and outflow stenosis with an MLD of ⩽1.9 mm at vascular access sites, sensitivity = 86.00% and 88.46%; specificity = 97.67% and 92.11%; positive predictive values of 97.73% and 92.00% and negative predictive values of 85.71% and 88.61%, respectively, were observed. Conclusions: Our preliminary results showed that physical examination can potentially be a diagnostic tool in detecting patients with stenosis who are at a high risk of thrombosis at hemodialysis vascular access sites with high diagnostic accuracy.
Cross-Calibration of Bone Mineral Densities and Body Composition between GE Lunar Prodigy and Osteosys Primus

Background The aim of this study was to investigate the correlation between bone mineral density (BMD) and body composition measured by the Osteosys Primus® and the GE Lunar Prodigy® and to calculate the conversion rate between the 2 devices. Methods The 40 subjects were men and women in aged 20 to 29 years old. All participants were scanned twice on both the Osteosys Primus (OsteoSys) and the GE Lunar Prodigy (GE Healthcare) DXA systems using the manufacturers’ standard scanning and positioning protocols. Results Compared to the GE Lunar device, the mean Osteosys fat mass was overestimated to be 12.1% (1,776.9 g) in the whole body, 5.1% (163.9 g) in gynoid, and 6.7% (87.2 g) in android. Compared with the GE Lunar device, the mean BMDs of the Osteosys Primus were underestimated to be 2.3% (0.023 g/cm2) in the whole body and 3.1% (0.035 g/cm2) in L1-4. Compared with the GE Lunar device, the mean lean mass derived by the Osteosys Primus were underestimated to 2.3% (1,045.3 g) in the total body, 3.8% (179.4 g) in arms, and 7.7% (1,104.8 g) in legs, respectively. There were a strong correlation of BMD and body composition between both groups. Conclusions Linear correction equations were developed to ensure comparability of BMD and muscle mass between the Osteosys Primus and the GE Lunar Prodigy. Importantly, use of equations from previous studies would have increased the discrepancy between the Osteosys Primus and the GE Lunar Prodigy.
Applications of Capacitive Micromachined Ultrasonic Transducers: A Comprehensive Review

Capacitive micromachined ultrasonic transducer (CMUT) was introduced as an alternative to the piezoelectric thick-film-based transducers in medical imaging applications. Gradually, CMUTs have been investigated in almost all the applications in acoustics due to their superior transduction properties. CMOS compatible process flow and limitless possibilities of miniaturization made CMUT a preferred choice for the ultrasound industry. This article comprehensively reviews all the applications in which CMUT was used until now. Such a complete review of the practical applications of CMUT has not been reported elsewhere. A topicwise presentation approach is adopted, and wherever possible, the necessary details of the device properties and experimental niceties were briefly covered.
Longitudinal Dynamics of a Blood Transcriptomic Signature of Tuberculosis

Rationale Performance of blood transcriptomic tuberculosis (TB) signatures in longitudinal studies and effects of TB-preventive therapy and coinfection with HIV or respiratory organisms on transcriptomic signatures has not been systematically studied. Objectives We evaluated longitudinal kinetics of an 11-gene blood transcriptomic TB signature, RISK11, and effects of TB-preventive therapy (TPT) and respiratory organisms on RISK11 signature score, in HIV-uninfected and HIV-infected individuals. Methods RISK11 was measured in a longitudinal study of RISK11-guided TPT in HIV-uninfected adults, a cross-sectional respiratory organisms cohort, or a longitudinal study in people living with HIV (PLHIV). HIV-uninfected RISK11+ participants were randomized to TPT or no TPT; RISK11− participants received no TPT. PLHIV received standard-of-care antiretroviral therapy and TPT. In the cross-sectional respiratory organisms cohort, viruses and bacteria in nasopharyngeal and oropharyngeal swabs were quantified by real-time quantitative PCR. Measurements and Main Results RISK11+ status was transient in most of the 128 HIV-negative participants with longitudinal samples; more than 70% of RISK11+ participants reverted to RISK11− by 3 months, irrespective of TPT. By comparison, reversion from a RISK11+ state was less common in 645 PLHIV (42.1%). Non-HIV viral and nontuberculous bacterial organisms were detected in 7.2% and 38.9% of the 1,000 respiratory organisms cohort participants, respectively, and among those investigated for TB, 3.8% had prevalent disease. Median RISK11 scores (%) were higher in participants with viral organisms alone (46.7%), viral and bacterial organisms (42.8%), or prevalent TB (85.7%) than those with bacterial organisms other than TB (13.4%) or no organisms (14.2%). RISK11 could not discriminate between prevalent TB and viral organisms. Conclusions Positive RISK11 signature status is often transient, possibly due to intercurrent viral infection, highlighting potentially important challenges for implementation of these biomarkers as new tools for TB control.