BMAD: Benchmarks for Medical Anomaly Detection

Anomaly detection (AD) is a fundamental research problem in machine learning and computer vision, with practical applications in industrial inspection, video surveillance, and medical diagnosis. In medical imaging, AD is especially vital for detecting and diagnosing anomalies that may indicate rare diseases or conditions. However, there is a lack of a universal and fair benchmark for evaluating AD methods on medical images, which hinders the development of more generalized and robust AD methods in this specific domain. To bridge this gap, we introduce a comprehensive evaluation benchmark for assessing anomaly detection methods on medical images. This benchmark encompasses six reorganized datasets from five medical domains (i.e. brain MRI, liver CT, retinal OCT, chest X-ray, and digital histopathology) and three key evaluation metrics, and includes a total of fourteen state-of-the-art AD algorithms. This standardized and well-curated medical benchmark with the well-structured codebase enables comprehensive comparisons among recently proposed anomaly detection methods. It will facilitate the community to conduct a fair comparison and advance the field of AD on medical imaging. More information on BMAD is available in our GitHub repository: https://github.com/DorisBao/BMA

Novel Y-chromosomal microdeletions associated with non-obstructive azoospermia uncovered by high throughput sequencing of sequence-tagged sites (STSs)

Y-chromosomal microdeletion (YCM) serves as an important genetic factor in non-obstructive azoospermia (NOA). Multiplex polymerase chain reaction (PCR) is routinely used to detect YCMs by tracing sequence-tagged sites (STSs) in the Y chromosome. Here we introduce a novel methodology in which we sequence 1,787 (post-filtering) STSs distributed across the entire male-specific Y chromosome (MSY) in parallel to uncover known and novel YCMs. We validated this approach with 766 Chinese men with NOA and 683 ethnically matched healthy individuals and detected 481 and 98 STSs that were deleted in the NOA and control group, representing a substantial portion of novel YCMs which significantly influenced the functions of spermatogenic genes. The NOA patients tended to carry more and rarer deletions that were enriched in nearby intragenic regions. Haplogroup O2* was revealed to be a protective lineage for NOA, in which the enrichment of b1/b3 deletion in haplogroup C was also observed. In summary, our work provides a new high-resolution portrait of deletions in the Y chromosome.National Key Scientific Program of China [2011CB944303]; National Nature Science Foundation of China [31271244, 31471344]; Promotion Program for Shenzhen Key Laboratory [CXB201104220045A]; Shenzhen Project of Science and Technology [JCYJ20130402113131202, JCYJ20140415162543017]SCI(E)[email protected]; [email protected]; [email protected]

Regulatory capacity building and the governance of clinical stem cell research in China

While other works have explained difficulties in applying ‘international’ guidelines in the field of regenerative medicine in so-called low- and middle-income countries (LMICs) in terms of ‘international hegemony’, ‘political and ethical governance’ and ‘cosmopolitisation’, this article on stem cell regulation in China emphasises the particular complexities faced by large LMICs: the emergence of alternative regulatory arrangements made by stakeholders at a provincial level at home. On the basis of ethnographic and archival research of clinical stem cell research hubs, we have characterized six types of entrepreneurial ‘bionetworks’, each of which embodies a regulatory orientation that developed in interaction with China’s regulatory dilemmas. Rather than adopting guidelines from other countries, we argue that regulatory capacity building is more appropriately viewed as a relational concept, referring to the ability to develop regulatory requirements that can cater for different regulatory research needs on an international level and at home

Novel loci and pathways significantly associated with longevity

Only two genome-wide significant loci associated with longevity have been identified so far, probably because of insufficient sample sizes of centenarians, whose genomes may harbor genetic variants associated with health and longevity. Here we report a genome-wide association study (GWAS) of Han Chinese with a sample size 2.7 times the largest previously published GWAS on centenarians. We identified 11 independent loci associated with longevity replicated in Southern-Northern regions of China, including two novel loci (rs2069837-IL6; rs2440012-ANKRD20A9P) with genome-wide significance and the rest with suggestive significance (P < 3.65 × 10(−5)). Eight independent SNPs overlapped across Han Chinese, European and U.S. populations, and APOE and 5q33.3 were replicated as longevity loci. Integrated analysis indicates four pathways (starch, sucrose and xenobiotic metabolism; immune response and inflammation; MAPK; calcium signaling) highly associated with longevity (P ≤ 0.006) in Han Chinese. The association with longevity of three of these four pathways (MAPK; immunity; calcium signaling) is supported by findings in other human cohorts. Our novel finding on the association of starch, sucrose and xenobiotic metabolism pathway with longevity is consistent with the previous results from Drosophilia. This study suggests protective mechanisms including immunity and nutrient metabolism and their interactions with environmental stress play key roles in human longevity

Novel loci and pathways significantly associated with longevity

Only two genome-wide significant loci associated with longevity have been identified so far, probably because of insufficient sample sizes of centenarians, whose genomes may harbor genetic variants associated with health and longevity. Here we report a genome-wide association study (GWAS) of Han Chinese with a sample size 2.7 times the largest previously published GWAS on centenarians. We identified 11 independent loci associated with longevity replicated in Southern-Northern regions of China, including two novel loci (rs2069837-IL6; rs2440012-ANKRD20A9P) with genome-wide significance and the rest with suggestive significance (P < 3.65 × 10⁻⁵). Eight independent SNPs overlapped across Han Chinese, European and U.S. populations, and APOE and 5q33.3 were replicated as longevity loci. Integrated analysis indicates four pathways (starch, sucrose and xenobiotic metabolism; immune response and inflammation; MAPK; calcium signaling) highly associated with longevity (P ≤ 0.006) in Han Chinese. The association with longevity of three of these four pathways (MAPK; immunity; calcium signaling) is supported by findings in other human cohorts. Our novel finding on the association of starch, sucrose and xenobiotic metabolism pathway with longevity is consistent with the previous results from Drosophilia. This study suggests protective mechanisms including immunity and nutrient metabolism and their interactions with environmental stress play key roles in human longevity.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Nature Publishing Group. The published article can be found at: http://www.nature.com/articles/srep2124

A self-breaking supramolecular plugging system as lost circulation material in oilfield

Lost circulation is a frequently encountered problem during workover operations of a low-pressure reservoir. Many lost circulation materials (LCM) have been used to solve the problem, but various disadvantages still exist, for example, oil-soluble materials are easy to get stuck in the pipe string as the temperature drops and gel time and gel strength of the cross-linking gel systems are difficult to control in the occasion of inadequate stirring. A self-breaking supramolecular plugging system used to control lost circulation of workover operations is developed, and it can encounter the aforementioned disadvantages of the traditional LCM. The system forms a space grid structure by non-covalent bonds between the molecules without adding a cross-linking agent. Sand beds plugged with the supramolecular plugging system had a pressure bearing capacity of 4.5 MPa. The self-breaking rate of the supramolecular system was 100% after 7 days at a temperature of 120°C. The core permeability recovery of the self-breaking liquid was 91.9%, indicated that the plugging system is compatible of the reservoir. The supramolecular plugging system has been used in four wells in the Jidong oilfield of East China. Field practice showed that the supramolecular LCM can effectively control lost circulation at different rates during workover operations. The increase in the daily fluid after operations indicated that the slurry has not damaged the reservoir

Influencing Factors of Cutting Force for Apple Tree Branch Pruning

Apple, which occupies the first position in the world with regard to its yield, is an important economic crop in China. Pruning of apple trees is still dominated by manual pruning, resulting in high labor costs and low efficiency. Additionally, there are some limitations with pruning machines. Thus, research regarding the mechanical properties of apple branches is the basis for the designing proper pruning machine. This paper aims to study the effect of the feed rate, cutting line speed, branch diameter, and moisture content on the cutting force. Results revealed that cutting force depended on the feed rate, cutting line speed, and branch diameter. Furthermore, both the cutting line speed and the branch diameter had a significant effect on the cutting force (p p > 0.05). However, the moisture content had no effect on the cutting force, with a difference of cutting force between samples with moisture content of 15% and 50% less than 5%. Based on the experiments performed, an equation relating the feed rate, the cutting line speed, the branch diameter was derived to calculate the cutting force. By verification test, it established that regression equation was valid with error less than 4%. This study explored the mechanical properties of apple branch, and obtained the optimal cutting parameters, which can provide a reference for the design of the pruning machine

Influencing Factors of Cutting Force for Apple Tree Branch Pruning

Apple, which occupies the first position in the world with regard to its yield, is an important economic crop in China. Pruning of apple trees is still dominated by manual pruning, resulting in high labor costs and low efficiency. Additionally, there are some limitations with pruning machines. Thus, research regarding the mechanical properties of apple branches is the basis for the designing proper pruning machine. This paper aims to study the effect of the feed rate, cutting line speed, branch diameter, and moisture content on the cutting force. Results revealed that cutting force depended on the feed rate, cutting line speed, and branch diameter. Furthermore, both the cutting line speed and the branch diameter had a significant effect on the cutting force (p &lt; 0.01), while the feed rate had a small effect on the cutting force (p &gt; 0.05). However, the moisture content had no effect on the cutting force, with a difference of cutting force between samples with moisture content of 15% and 50% less than 5%. Based on the experiments performed, an equation relating the feed rate, the cutting line speed, the branch diameter was derived to calculate the cutting force. By verification test, it established that regression equation was valid with error less than 4%. This study explored the mechanical properties of apple branch, and obtained the optimal cutting parameters, which can provide a reference for the design of the pruning machine

The Discovery of Natural Typing Annotations: User-produced Potential Chinese Word Delimiters

Human labeled corpus is indispensable for the training of supervised word segmenters. However, it is time-consuming and labor-intensive to label corpus manually. During the process of typing Chinese text by Pingyin, people usually need to type &quot;space &quot; or nu-meric keys to choose the words due to homo-phones, which can be viewed as a cue for segmentation. We argue that such a process can be used to build a labeled corpus in a more natural way. Thus, in this paper, we in-vestigate Natural Typing Annotations (NTAs) that are potential word delimiters produced by users while typing Chinese. A detailed analysis on over three hundred user-produced texts containing NTAs reveals that high-quality NTAs mostly agree with gold seg-mentation and, consequently, can be used for improving the performance of supervised word segmentation model in out-of-domain. Experiments show that a classification model combined with a voting mechanism can reli-ably identify the high-quality NTAs texts that are more readily available labeled corpus. Furthermore, the NTAs might be particularly useful to deal with out-of-vocabulary (OOV) words such as proper names and neo-logisms.