Classes Are Not Equal: An Empirical Study on Image Recognition Fairness

In this paper, we present an empirical study on image recognition fairness, i.e., extreme class accuracy disparity on balanced data like ImageNet. We experimentally demonstrate that classes are not equal and the fairness issue is prevalent for image classification models across various datasets, network architectures, and model capacities. Moreover, several intriguing properties of fairness are identified. First, the unfairness lies in problematic representation rather than classifier bias. Second, with the proposed concept of Model Prediction Bias, we investigate the origins of problematic representation during optimization. Our findings reveal that models tend to exhibit greater prediction biases for classes that are more challenging to recognize. It means that more other classes will be confused with harder classes. Then the False Positives (FPs) will dominate the learning in optimization, thus leading to their poor accuracy. Further, we conclude that data augmentation and representation learning algorithms improve overall performance by promoting fairness to some degree in image classification. The Code is available at https://github.com/dvlab-research/Parametric-Contrastive-Learning.Comment: CVPR 202

Agouti C57BL/6N embryonic stem cells for mouse genetic resources.

We report the characterization of a highly germline competent C57BL/6N mouse embryonic stem cell line, JM8. To simplify breeding schemes, the dominant agouti coat color gene was restored in JM8 cells by targeted repair of the C57BL/6 nonagouti mutation. These cells provide a robust foundation for large-scale mouse knockout programs that aim to provide a public resource of targeted mutations in the C57BL/6 genetic background

Assessment of the feasibility and coverage of a modified universal hearing screening protocol for use with newborn babies of migrant workers in Beijing

BACKGROUND: Although migrant workers account for the majority of newborns in Beijing, their children are less likely to undergo appropriate universal newborn hearing screening/rescreening (UNHS) than newborns of local non-migrant residents. We hypothesised that this was at least in part due to the inadequacy of the UNHS protocol currently employed for newborn babies, and therefore aimed to modify the protocol to specifically reflect the needs of the migrant population. METHODS: A total of 10,983 healthy babies born to migrant mothers between January 2007 and December 2009 at a Beijing public hospital were investigated for hearing abnormalities according to a modified UNHS protocol. This incorporated two additional/optional otoacoustic emissions (OAE) tests at 24–48 hours and 2 months after birth. Infants not passing a screening test were referred to the next test, until any hearing loss was confirmed by the auditory brainstem response (ABR) test. RESULTS: A total of 98.91% (10983/11104) of all newborn children underwent the initial OAE test, of which 27.22% (2990/10983) failed the test. 1712 of the failed babies underwent the second inpatient OAE test, with739 failing again; thus significantly decreasing the overall positive rate for abnormal hearing from 27.22% to 18.36% ([2990–973 /10983)]; p = 0). Overall, 1147(56.87%) babies underwent the outpatient OAE test again after1-month, of whom 228 failed and were referred for the second outpatient OAE test (i.e. 2.08% (228/10983) referral rate at 1month of age). 141 of these infants underwent the referral test, of whom 103 (73.05%) tested positive again and were referred for a final ABR test for hearing loss (i.e. final referral rate of 1.73% ([228-38/10983] at 2 months of age). Only 54 infants attended the ABR test and 35 (0.32% of the original cohort tested) were diagnosed with abnormal hearing. CONCLUSIONS: Our study shows that it is feasible and practical to achieve high coverage rates for screening hearing loss and decrease the referral rates in newborn babies of migrant workers, using a modification of the currently employed UNHS protocol

Automated segmentation of normal and diseased coronary arteries – The ASOCA challenge

Cardiovascular disease is a major cause of death worldwide. Computed Tomography Coronary Angiography (CTCA) is a non-invasive method used to evaluate coronary artery disease, as well as evaluating and reconstructing heart and coronary vessel structures. Reconstructed models have a wide array of for educational, training and research applications such as the study of diseased and non-diseased coronary anatomy, machine learning based disease risk prediction and in-silico and in-vitro testing of medical devices. However, coronary arteries are difficult to image due to their small size, location, and movement, causing poor resolution and artefacts. Segmentation of coronary arteries has traditionally focused on semi-automatic methods where a human expert guides the algorithm and corrects errors, which severely limits large-scale applications and integration within clinical systems. International challenges aiming to overcome this barrier have focussed on specific tasks such as centreline extraction, stenosis quantification, and segmentation of specific artery segments only. Here we present the results of the first challenge to develop fully automatic segmentation methods of full coronary artery trees and establish the first large standardized dataset of normal and diseased arteries. This forms a new automated segmentation benchmark allowing the automated processing of CTCAs directly relevant for large-scale and personalized clinical applications

Self-renewal and chemotherapy resistance of p75NTR positive cells in esophageal squamous cell carcinomas

<p>Abstract</p> <p>Background</p> <p>p75^NTRhas been used to isolate esophageal and corneal epithelial stem cells. In the present study, we investigated the expression of p75^NTRin esophageal squamous cell carcinoma (ESCC) and explored the biological properties of p75^NTR+cells.</p> <p>Methods</p> <p>p75^NTRexpression in ESCC was assessed by immunohistochemistry. p75^NTR+and p75^NTR-cells of 4 ESCC cell lines were separated by fluorescence-activated cell sorting. Differentially expressed genes between p75^NTR+and p75^NTR-cells were determined by real-time quantitative reverse transcription-PCR. Sphere formation assay, DDP sensitivity assay, ⁶⁴copper accumulation assay and tumorigenicity analysis were performed to determine the capacity of self-renewal, chemotherapy resistance and tumorigenicity of p75^NTR+cells.</p> <p>Results</p> <p>In ESCC specimens, p75^NTRwas found mainly confined to immature cells and absent in cells undergoing terminal differentiation. The percentage of p75^NTR+cells was 1.6%–3.7% in Eca109 and 3 newly established ESCC cell lines. The expression of Bmi-1, which is associated with self-renewal of stem cells, was significantly higher in p75^NTR+cells. p63, a marker identified in keratinocyte stem cells, was confined mainly to p75^NTR+cells. The expression of CTR1, which is associated with cisplatin (DDP)-resistance, was significantly decreased in p75^NTR+cells. Expression levels of differentiation markers, such as involucrin, cytokeratin 13, β1-integrin and β4-integrin, were lower in p75^NTR+cells. In addition, p75^NTR+cells generated both p75^NTR+and p75^NTR-cells, and formed nonadherent spherical clusters in serum-free medium supplemented with growth factors. Furthermore, p75^NTR+cells were found to be more resistant to DDP and exhibited lower ⁶⁴copper accumulation than p75^NTR-cells.</p> <p>Conclusion</p> <p>Our results demonstrated that p75^NTR+cells possess some characteristics of CSCs, namely, self-renewal and chemotherapy resistance. Chemotherapy resistance of p75^NTR+cells may probably be attributable to decreased expression of CTR1.</p

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).Peer reviewe

The evolution of cyclodextrin glucanotransferase product specificity

Cyclodextrin glucanotransferases (CGTases) have attracted major interest from industry due to their unique capacity of forming large quantities of cyclic α-(1,4)-linked oligosaccharides (cyclodextrins) from starch. CGTases produce a mixture of cyclodextrins from starch consisting of 6 (α), 7 (β) and 8 (γ) glucose units. In an effort to identify the structural factors contributing to the evolutionary diversification of product specificity amongst this group of enzymes, we selected nine CGTases from both mesophilic, thermophilic and hyperthermophilic organisms for comparative product analysis. These enzymes displayed considerable variation regarding thermostability, initial rates, percentage of substrate conversion and ratio of α-, β- and γ-cyclodextrins formed from starch. Sequence comparison of these CGTases revealed that specific incorporation and/or substitution of amino acids at the substrate binding sites, during the evolutionary progression of these enzymes, resulted in diversification of cyclodextrin product specificity

A chromosome conformation capture ordered sequence of the barley genome

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Anti-podocalyxin antibody exerts antitumor effects via antibody-dependent cellular cytotoxicity in mouse xenograft models of oral squamous cell carcinoma

Podocalyxin (PODXL) overexpression is associated with progression, metastasis, and poor outcomes in cancers. We recently produced the novel anti-PODXL monoclonal antibody (mAb) PcMab-47 (IgG1, kappa). Herein, we engineered PcMab-47 into 47-mG2a, a mouse IgG2a-type mAb, to add antibody-dependent cellular cytotoxicity (ADCC). We further developed 47-mG2a-f, a core fucose-deficient type of 47-mG2a to augment its ADCC. Immunohistochemical analysis of oral cancer tissues using PcMab-47 and 47-mG2a revealed that the latter stained oral squamous cell carcinoma (OSCC) cells in a cytoplasmic pattern at a much lower concentration. PcMab-47 and 47-mG2a detected PODXL in 163/201 (81.1%) and in 197/201 (98.0%) OSCC samples, respectively. 47-mG2a-f also detected PODXL in OSCCs at a similar frequency as 47-mG2a. In vitro analysis revealed that both 47-mG2a and 47-mG2a-f exhibited strong complement-dependent cytotoxicity (CDC) against CHO/hPODXL cells. In contrast, 47-mG2a-f exhibited much stronger ADCC than 47-mG2a against OSCC cells, indicating that ADCC and CDC of those anti-PODXL mAbs depend on target cells. In vivo analysis revealed that both 47-mG2a and 47-mG2a-f exerted antitumor activity in CHO/hPODXL xenograft models at a dose of 100 μg or 500 μg/mouse/week administered twice. 47-mG2a-f, but not 47-mG2a, exerted antitumor activity in SAS and HSC-2 xenograft models at a dose of 100 μg/mouse/week administered three times. Although both 47-mG2a and 47-mG2a-f exerted antitumor activity in HSC-2 xenograft models at a dose of 500 μg/mouse/week administered twice, 47-mG2a-f also showed higher antitumor activity than 47-mG2a. These results suggested that a core fucose-deficient anti-PODXL mAb could be useful for antibody-based therapy against PODXL-expressing OSCCs