Miracle-dz/UniFAR-FTUs huggingface dataset:
Host-parasite interaction explains variation in the prevalence of avian haemosporidians at the community level

Parasites are a selective force that shape host community structure and dynamics, but host communities can also influence parasitism. Understanding the dual nature from host-parasite interactions can be facilitated by quantifying the variation in parasite prevalence among host species and then comparing that variation to other ecological factors that are known to also shape host communities. Avian haemosporidian parasites (e.g. Plasmodium and Haemoproteus) are abundant and widespread representing an excellent model for the study of host-parasite interactions. Several geographic and environmental factors have been suggested to determine prevalence of avian haemosporidians in bird communities. However, it remains unknown whether host and parasite traits, represented by phylogenetic distances among species and degree of specialization in host-parasite relationships, can influence infection status. The aims of this study were to analyze factors affecting infection status in a bird community and to test whether the degree of parasite specialization on their hosts is determined by host traits. Our statistical analyses suggest that infection status is mainly determined by the interaction between host species and parasite lineages where tolerance and/or susceptibility to parasites plays an essential role. Additionally, we found that although some of the parasite lineages infected a low number of bird individuals, the species they infected were distantly related and therefore the parasites themselves should not be considered typical host specialists. Infection status was higher for generalist than for specialist parasites in some, but not all, host species. These results suggest that detected prevalence in a species mainly results from the interaction between host immune defences and parasite exploitation strategies wherein the result of an association between particular parasite lineages and particular host species is idiosyncratic.
Genomic Variations in Susceptibility to Intracranial Aneurysm in the Korean Population

Genome-wide association studies found genetic variations with modulatory effects for intracranial aneurysm (IA) formations in European and Japanese populations. We aimed to identify the susceptibility of single nucleotide polymorphisms (SNPs) to IA in a Korean population consisting of 250 patients, and 294 controls using the Asian-specific Axiom Precision Medicine Research Array. Twenty-nine SNPs reached a genome-wide significance threshold (5 × 10−8). The rs371331393 SNP, with a stop-gain function of ARHGAP32 (11q24.3), showed the most significant association with the risk of IA (OR = 43.57, 95% CI: 21.84–86.95; p = 9.3 × 10−27). Eight out of 29 SNPs—GBA (rs75822236), TCF24 (rs112859779), OLFML2A (rs79134766), ARHGAP32 (rs371331393), CD163L1 (rs138525217), CUL4A (rs74115822), LOC102724084 (rs75861150), and LRRC3 (rs116969723)—demonstrated sufficient statistical power greater than or equal to 0.8. Two previously reported SNPs, rs700651 (BOLL, 2q33.1) and rs6841581 (EDNRA, 4q31.22), were validated in our GWAS (Genome-wide association study). In a subsequent analysis, three SNPs showed a significant difference in expressions: the rs6741819 (RNF144A, 2p25.1) was down-regulated in the adrenal gland tissue (p = 1.5 × 10−6), the rs1052270 (TMOD1. 9q22.33) was up-regulated in the testis tissue (p = 8.6 × 10−10), and rs6841581 (EDNRA, 4q31.22) was up-regulated in both the esophagus (p = 5.2 × 10−12) and skin tissues (1.2 × 10−6). Our GWAS showed novel candidate genes with Korean-specific variations in IA formations. Large population based studies are thus warranted.
Benchmark on Automatic Six-Month-Old Infant Brain Segmentation Algorithms: The iSeg-2017 Challenge

Accurate segmentation of infant brain magnetic resonance (MR) images into white matter (WM), gray matter (GM), and cerebrospinal fluid is an indispensable foundation for early studying of brain growth patterns and morphological changes in neurodevelopmental disorders. Nevertheless, in the isointense phase (approximately 6–9 months of age), due to inherent myelination and maturation process, WM and GM exhibit similar levels of intensity in both T1-weighted and T2-weighted MR images, making tissue segmentation very challenging. Although many efforts were devoted to brain segmentation, only a few studies have focused on the segmentation of six-month infant brain images. With the idea of boosting methodological development in the community, iSeg-2017 challenge (http://iseg2017.web.unc.edu) provides a set of six-month infant subjects with manual labels for training and testing the participating methods. Among the 21 automatic segmentation methods participating in iSeg-2017, we review the eight top-ranked teams, in terms of Dice ratio, modified Hausdorff distance, and average surface distance, and introduce their pipelines, implementations, as well as source codes. We further discuss the limitations and possible future directions. We hope the dataset in iSeg-2017, and this paper could provide insights into methodological development for the community.
A systematic survey of the sodium contents of processed foods.

BACKGROUND Processed foods are major contributors to population dietary salt intake. Parts of the Australian food industry have started to decrease salt in a number of products. A definitive baseline assessment of current sodium concentrations in foods is key to targeting reformulation strategies and monitoring progress. OBJECTIVES Our objectives were to systematically collate data on the sodium content of Australian processed food products and compare sodium values against maximum target levels established by the UK Food Standards Agency (UK FSA). DESIGN Categories of processed foods that contribute the majority of salt to Australian diets were identified. Food-composition data were sought for all products in these categories, and the sodium content in mg/100 g (or mg/100 mL for liquids) was recorded for each. Mean sodium values were calculated for each grouping and compared with the UK FSA benchmarks. RESULTS Sodium data were collected for 7221 products in 10 food groups, 33 food categories, and 90 food subcategories. The food groups that were highest in sodium were sauces and spreads (1283 mg/100 g) and processed meats (846 mg/100 g). Cereal and cereal products (206 mg/100 g) and fruit and vegetables (211 mg/100 g) were the lowest in sodium. Sixty-three percent of food categories had mean sodium concentrations above the UK FSA targets, and most had wide ranges between the most and least salty product. CONCLUSIONS Many products, particularly breads, processed meats, and sauces, have salt amounts above reasonable benchmarks. The variation in salt concentrations between comparable products suggests that reformulation is highly feasible for many foods.
Influenza-Related Communication and Community Mitigation Strategies: Results From the 2015 Pandemic Influenza Readiness Assessment

Emergence of a novel infectious disease, such as pandemic influenza, is the one global crisis most likely to affect the greatest number of people worldwide. Because of the potentially severe and contagious nature of influenza, a rapid multifaceted pandemic response, which includes nonpharmaceutical interventions (NPIs) and effective strategies for communication with the public are essential for a timely response and mitigating the spread of disease. A web-based questionnaire was administered via email in July 2015 to 62 Public Health Emergency Preparedness (PHEP) directors across jurisdictions that receive funding through the Centers for Disease Control and Prevention PHEP cooperative agreement. This report focuses on two modules: Public Information and Communication and Community Mitigation. Consistent and targeted communication are critical for the acceptability and success of NPIs. All 62 jurisdictions have developed or are in the process of developing a communications plan. Community-level NPIs such as home isolation, school closures, and respiratory etiquette play a critical role in mitigating the spread of disease. Effective, ongoing communication with the public is essential to ensuring wide spread compliance of NPI’s, especially among non–English-speaking populations. Planning should also include reaching vulnerable populations and identifying the correct legal authorities for closing schools and canceling mass gatherings.
Peer-Victimization of Young Children With Developmental and Behavioral Difficulties-A Population-Based Study.

OBJECTIVE The aim is to investigate if young children with developmental and behavioral difficulties (DBDs) have greater risk of peer-victimization compared with typically developing (TD) children. METHOD The sample was drawn from the Norwegian Mother and Child Cohort Study (MoBa). MoBa has collected population-based data on children's health and development for 114,500 children. We included children that were 5 years of age (n = 41,609). Multivariate logistic regression was used to estimate the effect of different DBDs and of co-occurring DBDs on peer-victimization compared with TD children. Categories of DBDs included autistic traits, emotional difficulties, behavioral difficulties, general learning difficulties, attention difficulties/impulsive behavior, motor development difficulties, language difficulties, and hearing and vision difficulties. Results were adjusted for socioeconomic status and the child's sex. RESULTS Peer-victimization was 2.8% (933) among TD children, and 8.0% (615) among children with DBD. The highest risk of peer-victimization was found among children with autistic traits and children with five or more co-occurring DBDs (adjusted odds ratios [ORs] = 12.76; 95% confidence interval [CI] 8.64-18.84; p ≤ .001) and 17.37 (95% CI 12.15-24.82; p ≤ .001)], respectively. The lowest risk was found among children with hearing and vision difficulties and children with only one DBD [adjusted ORs = 1.98 (95% CI 1.71-2.29; p ≤ .001) and 1.95 (95% CI 1.70-2.22; p ≤ .001)]. CONCLUSION Children with DBD have a substantially higher risk of peer-victimization compared with TD children. Peer-victimization varies with type of DBD and increases cumulatively by number of DBDs.
Development and Validation of a Nomogram for Preoperative Prediction of Perineural Invasion in Colorectal Cancer

Background In colorectal cancer (CRC), perineural invasion (PNI) is usually identified histologically in biopsy or resection specimens and is considered a high-risk feature for recurrence of CRC and is an indicator for adjuvant therapy. Preoperative identification of PNI could help determine the need for adjuvant therapy and the approach to surgical resection. This study aimed to develop and validate a nomogram for the preoperative prediction of PNI in patients with CRC. Material/Methods A total of 664 patients with CRC from a single center were classified into a training dataset (n=468) and a validation dataset (n=196). The least absolute shrinkage and selection operator (LASSO) regression model was used to select potentially relevant features. Multivariate logistic regression analysis was used to develop the nomogram. The performance of the nomogram was assessed based on its calibration, discrimination, and clinical utility. Results The nomogram consisted of five clinical features and provided good calibration and discrimination in the training dataset, with an area under the curve (AUC) of 0.704 (95% CI, 0.657–0.751). Application of the nomogram in the validation cohort showed acceptable discrimination, with the AUC of 0.692 (95% CI, 0.617–0.766) and good calibration. Decision curve analysis (DCA) showed that the nomogram was clinically useful. Conclusions The nomogram developed in this study might allow clinicians to predict the risk of PNI in patients with CRC preoperatively. The nomogram showed favorable discrimination and calibration values, which may help optimize preoperative treatment decision-making for patients with CRC.
A Deep Convolutional Neural Network Inspired by Auditory Perception for Underwater Acoustic Target Recognition

Underwater acoustic target recognition (UATR) using ship-radiated noise faces big challenges due to the complex marine environment. In this paper, inspired by neural mechanisms of auditory perception, a new end-to-end deep neural network named auditory perception inspired Deep Convolutional Neural Network (ADCNN) is proposed for UATR. In the ADCNN model, inspired by the frequency component perception neural mechanism, a bank of multi-scale deep convolution filters are designed to decompose raw time domain signal into signals with different frequency components. Inspired by the plasticity neural mechanism, the parameters of the deep convolution filters are initialized randomly, and the is n learned and optimized for UATR. The n, max-pooling layers and fully connected layers extract features from each decomposed signal. Finally, in fusion layers, features from each decomposed signal are merged and deep feature representations are extracted to classify underwater acoustic targets. The ADCNN model simulates the deep acoustic information processing structure of the auditory system. Experimental results show that the proposed model can decompose, model and classify ship-radiated noise signals efficiently. It achieves a classification accuracy of 81.96%, which is the highest in the contrast experiments. The experimental results show that auditory perception inspired deep learning method has encouraging potential to improve the classification performance of UATR.
CD5+ B lymphocytes secrete IL-10 rather than TGF-β1 which control the immune response in autoimmune haemolytic anaemia/Evans syndrome

Abstract Objective: To investigate the quantity and secretion function of cytokines-secreted CD5+ B lymphocytes in Autoimmune Haemolytic Anaemia (AIHA)/Evans syndrome (ES) patients. Methods: Twenty-five untreated AIHA/ES patients, 28 remission AIHA/ES patients and 25 healthy controls (HCs) were enrolled in this study. The quantity of CD5+B lymphocytes which produce interleukin-10 (IL-10) (CD5+IL-10+) and transforming growth factor (TGF-β1) (CD5+TGF-β1+) were detected by flow cytometry (FCM). CD5+ B lymphocytes were sorted from peripheral blood (PB) by FCM and the expression of IL-10 and TGF-β1 mRNA in CD5+ B cells were measured by real-time PCR (RT-PCR). Results: The percentage of CD5+IL-10+B cells in CD5+ B lymphocytes in newly diagnosed patients was 82.18 ± 14.78%, which being significantly higher than that of remission AIHA/ES patients (56.68 ± 24.39%) and HCs (51.90 ± 22.95%) (p < .05). The percentage of CD5+IL-10+ B cells in CD5+ B lymphocytes in newly diagnosed patients was negatively correlated with haemoglobin (Hb), complement 3 (C3) (p < .05) and positively correlated with lactate dehydrogenase (LDH), total bilirubin (TBIL) and indirect unconjugated bilirubin (IBIL) (p < .05). The expression level of IL-10 mRNA in CD5+ B lymphocytes of newly diagnosed patients (49.34 ± 22.84) was higher than that of remission patients (3.97 ± 3.83) and HCs (1.78 ± 1.66) (p < .05). There was no significant difference among three groups with the proportion of CD5+TGF-β1+ B lymphocytes and the expression level of TGF-β1 mRNA in CD5+B lymphocytes (p > .05). Conclusions: CD5+ B lymphocytes could secrete IL-10 rather than TGF- β1 which control the immune response in AIHA/ES.
Active Surveillance Versus Nephron-Sparing Surgery for a Bosniak IIF or III Renal Cyst: A Cost-Effectiveness Analysis.

OBJECTIVE The objective of our study was to evaluate the cost-effectiveness of active surveillance (AS) versus nephron-sparing surgery (NSS) in patients with a Bosniak IIF or III renal cyst. MATERIALS AND METHODS Markov models were developed to estimate life expectancy and lifetime costs for 60-year-old patients with a Bosniak IIF or III renal cyst (the reference cases) managed by AS versus NSS. The models incorporated the malignancy rates, reclassification rates during follow-up, treatment effectiveness, complications and costs, and short- and long-term outcomes. An incremental cost-effectiveness analysis was performed to identify management preference under an assumed $75,000 per quality-adjusted life-year (QALY) societal willingness-to-pay threshold, using data from studies in the literature and the 2015 Medicare Physician Fee Schedule. The effects of key parameters were addressed in a multiway sensitivity analysis. RESULTS The prevalence of malignancy for Bosniak IIF and III renal cysts was 26% (25/96) and 52% (542/1046). Under base case assumptions for Bosniak IIF cysts, the incremental cost-effectiveness ratio of NSS relative to AS was $731,309 per QALY for women, exceeding the assumed societal willingness-to-pay threshold, and AS outperformed NSS for both life expectancy and cost for men. For Bosniak III cysts, AS yielded greater life expectancy (24.8 and 19.4 more days) and lower lifetime costs (cost difference of $12,128 and $11,901) than NSS for men and women, indicating dominance of AS over NSS. Superiority of AS held true in sensitivity analyses for men 46 years old or older and women 57 years old or older even when all parameters were set to favor NSS. CONCLUSION AS is more cost-effective than NSS for patients with a Bosniak IIF or III renal cyst.
Fatty Acid-Saturated Albumin Reduces High Mortality and Fluid Requirements In A Rat Model of Hemorrhagic Shock Plus Tourniquet and Hypotensive Resuscitation.

Military pre-hospital care for hemorrhage is often characterized by use of tourniquets (TQ) and permissive hypotensive resuscitation (PHR) with crystalloids or colloids, but these treatments have not been previously combined in an animal model. Although albumin resuscitation solutions have been tested, the potential effects of non-esterified fatty acids (NEFAs) bound to albumin have not been evaluated in vivo, and few studies have investigated concentrated albumin solutions to reduce fluid requirements. We created a militarily relevant rat model of trauma and hemorrhagic shock (T/HS) (27 ml/kg hemorrhage) with TQ and PHR. We investigated the ability of resuscitation with concentrated (250 mg/ml) albumin, followed by Plasmalyte as needed to maintain PHR, to reduce fluid volumes (vs. Plasmalyte alone, N = 17). Albumin was free of non-esterified fatty acids (N = 15) or saturated with oleic acid (OA; N = 13). The model resulted in high (53%) mortality within 3 hours of injury. Only OA-saturated albumin was able to significantly reduce mortality (from 47% to 8%) and fluid requirements (from 56 to 6 ml/kg) compared to Plasmalyte alone. Plasma NEFA-binding capacity was saturated earliest in the OA-saturated albumin group. Likewise, OA-saturated albumin tended to increase cell-free hemoglobin in the broncheoalveolar lavage fluid, which was significantly associated with survival. Our findings suggest incorporating TQ and PHR in T/HS models may result in high mortality and fluid requirements and that OA-saturated albumin, but not NEFA-free albumin or Plasmalyte alone, may provide a benefit to early survival and resuscitation volume, though a hemolytic mechanism may have later consequences, so caution is advised.
What fish can teach us about the feeding functions of postcranial muscles and joints.

Studies of vertebrate feeding have predominantly focused on the bones and muscles of the head, not the body. Yet, postcranial musculoskeletal structures like the spine and pectoral girdle are anatomically linked to the head, and may also have mechanical connections through which they can contribute to feeding. The feeding roles of postcranial structures have been best studied in ray-finned fishes, where the body muscles, vertebral column, and pectoral girdle attach directly to the head and help expand the mouth during suction feeding. Therefore, I use the anatomy and motion of the head-body interface in these fishes to develop a mechanical framework for studying postcranial functions during feeding. In fish the head and body are linked by the vertebral column, the pectoral girdle, and the body muscles that actuate these skeletal systems. The morphology of the joints and muscles of the cranio-vertebral and hyo-pectoral interfaces may determine the mobility of the head relative to the body, and ultimately the role of these interfaces during feeding. The postcranial interfaces can function as anchors during feeding: the body muscles and joints minimize motion between the head and body to stabilize the head or transmit forces from the body. Alternatively, the postcranial interfaces can be motors: body muscles actuate motion between the head and body to generate power for feeding motions. The motor function is likely important for many suction-feeding fishes, while the anchor function may be key for bite- or ram-feeding fishes. This framework can be used to examine the role of the postcranial interface in other vertebrate groups, and how that role changes (or not) with morphology and feeding behaviors. Such studies can expand our understanding of muscle function, as well as the evolution of vertebrate feeding behaviors across major transitions such as the invasion of land and the emergence of jaws.
Cross‐scale focus measure aggregation in depth recovery of microscopic objects

In shape from focus (SFF) methods, image focus volume enhancement is an important issue for acquiring accurate depth maps. Mostly, conventional approaches do focus aggregation locally to enhance the focus volume, which may not suppress noisy focus measurements properly and consequently, may provide deteriorated depth maps. Multiresolution fusion‐based method is proposed for image focus volume enhancement. First, an initial focus volume is obtained by applying a conventional focus measure. Then, a pyramid of focus volumes is computed using Gaussian filters and subsampling. Focus measures from various focus volumes at different levels are merged into a single resultant focus volume. Finally, the depth map is obtained from the resultant focus volume by maximizing the focus measure in the optical‐axis direction. According to the best of my knowledge, the cross‐scale aggregation has never been used in enhancing the image focus volume in SFF. The proposed method is evaluated through the experiments using image sequences of real microscopic and simulated objects. Results comparisons based on root mean square error (RMSE) and correlation demonstrate the effectiveness of the proposed method in improving the focus volume and depth map. The proposed fusion method of volumes is a simple but effective. The idea of cross‐scale aggregation of focus measures is effective in providing precise focus measures that consequently, provide accurate depth map. In future work, it will further be explored and a more sophisticated and optimization‐based fusion algorithm will be applied.