SANTA: Separate Strategies for Inaccurate and Incomplete Annotation Noise in Distantly-Supervised Named Entity Recognition

Distantly-Supervised Named Entity Recognition effectively alleviates the burden of time-consuming and expensive annotation in the supervised setting. But the context-free matching process and the limited coverage of knowledge bases introduce inaccurate and incomplete annotation noise respectively. Previous studies either considered only incomplete annotation noise or indiscriminately handle two types of noise with the same strategy. In this paper, we argue that the different causes of two types of noise bring up the requirement of different strategies in model architecture. Therefore, we propose the SANTA to handle these two types of noise separately with (1) Memory-smoothed Focal Loss and Entity-aware KNN to relieve the entity ambiguity problem caused by inaccurate annotation, and (2) Boundary Mixup to alleviate decision boundary shifting problem caused by incomplete annotation and a noise-tolerant loss to improve the robustness. Benefiting from our separate tailored strategies, we confirm in the experiment that the two types of noise are well mitigated. SANTA also achieves a new state-of-the-art on five public datasets.Comment: Findings of ACL202

In vivo evidence for the iron-binding activity of an iron-sulfur cluster assembly protein IscA in Escherichia coli

IscA is a key member of the iron-sulfur cluster assembly machinery in prokaryotic and eukaryotic organisms; however, the physiological function of IscA still remains elusive. In the present paper we report the in vivo evidence demonstrating the iron-binding activity of IscA in Escherichia coli cells. Supplement of exogenous iron (1 μM) in M9 minimal medium is sufficient to maximize the iron binding in IscA expressed in E. coli cells under aerobic growth conditions. In contrast, IscU, an iron-sulfur cluster assembly scaffold protein, or CyaY, a bacterial frataxin homologue, fails to bind any iron in E. coli cells under the same experimental conditions. Interestingly, the strong iron-binding activity of IscA is greatly diminished in E. coli cells under anaerobic growth conditions. Additional studies reveal that oxygen in medium promotes the iron binding in IscA, and that the iron binding in IscA in turn prevents formation of biologically inaccessible ferric hydroxide under aerobic conditions. Consistent with the differential iron-binding activity of IscA under aerobic and anaerobic conditions, we find that IscA and its paralogue SufA are essential for the iron-sulfur cluster assembly in E. coli cells under aerobic growth conditions, but not under anaerobic growth conditions. The results provide in vivo evidence that IscA may act as an iron chaperone for the biogenesis of iron-sulfur clusters in E. coli cells under aerobic conditions. © The Authors Journal compilation © 2010 Biochemical Society

Escherichia coli topoisomerase i is an iron and zinc binding protein

Escherichia coli topoisomerase I (TopA) cleaves and rejoins one strand of double-stranded DNA to relax the negatively supercoiled DNA. Structurally, TopA contains an N-terminal catalytic fragment and a C-terminal zinc-binding region that is required for relaxation of the negatively supercoiled DNA. Here we report that E. coli TopA is an iron and zinc binding protein. The UV-Vis absorption measurements and metal content analyses reveal that TopA purified from E. coli cells grown in the rich LB medium contains both iron and zinc. However, TopA purified from E. coli cells grown in the M9 minimal medium has negligible amounts of zinc or iron and no topoisomerase activity. Nevertheless, supplement of exogenous zinc or iron in E. coli cells grown in the M9 minimal medium produces the zinc- or iron-bound TopA, respectively. Whereas the zinc-bound TopA is fully active to relax the negatively supercoiled DNA, the iron-bound TopA has little or no enzyme activity. Furthermore, excess iron in the M9 minimal medium is able to compete with the zinc binding in TopA in E. coli cells and attenuate the topoisomerase activity, suggesting that E. coli TopA may be modulated by iron and zinc binding in vivo. © 2011 Springer Science+Business Media, LLC

Stimulated thyroglobulin and pre-ablation antithyroglobulin antibody products can predict the response to radioiodine therapy of TgAb-positive differentiated thyroid cancer patients: a retrospective study

ObjectiveWe aimed to explore the predictive value of stimulated thyroglobulin (sTg) and pre-ablation antithyroglobulin (pa-TgAb) products for the effect of radioiodine therapy (RAIT) on TgAb-positive differentiated thyroid cancer (DTC) patients.MethodsIn this study, we enrolled 265 patients with TgAb-positive DTC who underwent RAIT after total thyroidectomy (TT). Based on the last follow-up result, the patients were divided into two groups: the excellent response (ER) group and the non-excellent response (NER) group. We analyzed the factors related to the effect of RAIT.ResultsThe ER group consisted of 197 patients. The NER group consisted of 68 patients. For the univariate analysis, we found that the maximal tumor diameter, whether with extrathyroidal extension (ETE), bilateral or unilateral primary lesion, multifocality, preoperative TgAb (preop-TgAb), pa-TgAb, sTg × pa-TgAb, initial RAIT dose, N stage, and surgical extent (modified radical neck dissection or not), showed significant differences between the ER group and NER group (all p-values <0.05). The receiver operating characteristic (ROC) curves showed that the cutoff value was 724.25 IU/ml, 424.00 IU/ml, and 59.73 for preop-TgAb, pa-TgAb, and sTg × pa-TgAb, respectively. The multivariate logistic regression analysis results indicated that pa-TgAb, sTg × pa-TgAb, initial RAIT dose, and N stage were independent risk factors for NER (all p-values <0.05). For the Kaplan–Meier analysis of disease-free survival (DFS), the median DFS of the patients with sTg × pa-TgAb < 59.73 and initial RAIT dose ≤ 100 mCi was significantly longer than that of the patients with sTg × pa-TgAb ≥ 59.73 (50.27 months vs. 48.59 months, p = 0.041) and initial RAIT dose >100 mCi (50.50 months vs. 38.00 months, p = 0.030).ConclusionWe found the sTg and pa-TgAb conducts is a good predictor of the efficacy of RAIT in TgAb-positive DTC patients. It can play a very positive and important role in optimizing treatment, improving prognosis, and reducing the burden of patients

How well do Yao graph and Theta graph support Greedy Forwarding?

Greedy Forwarding algorithm is a widely-used routing algorithm for wireless networks. However, it can fail if the wireless network topologies contain voids, where a packet cannot be moved closer to destination. Since Yao graph and Theta graph are two types of geometric graphs exploited to construct wireless network topologies, this paper firstly studied whether these two types of graphs can contain voids, showing that when the number of cones in a Yao graph or Theta graph is less than six, Yao graph and Theta graph can have voids, and when the number of cones equals or exceeds six, Yao graph and Theta graph are free of voids. Secondly, this paper experimented on how well Greedy Forwarding is supported on Yao graphs and Theta graphs in terms of stretch, i.e., the ratio between the path length found by Greedy Forwarding and the shortest path length in a graph. The experiments also included comparison with the stretch on Delaunay triangulation, another well-known geometric graph exploited in constructing wireless networks. Overall, our experiments revealed several interesting results

POSTOPERATIVE RELATIONSHIP BETWEEN CELLULAR IMMUNE STATUS AND CLINICOPATHOLOGICAL CHARACTERISTICS IN DIFFERENTIATED THYROID CANCER PRIOR TO 131I THERAPY

Objective To investigate the postoperative relationship between cellular immune status and clinicopathological features in patients with differentiated thyroid carcinoma (DTC) before 131I therapy. Methods We retrospectively included 155 patients with DTC who had undergone total thyroidectomy with neck lymph node dissection plus 131I treatment 1-3 months after the operation in our hospital from March 2018 to February 2019. Peripheral blood natural killer (NK) cells and T cell subsets (CD3+ T cells, CD4+ T cells, CD8+ T cells, and CD4/CD8 ratio) were measured 1 d before 131I therapy. Univariable analysis was used to compare the cellular immunity indicators between patients with different clinicopathological features. Results The level of peripheral blood CD4+ T cells in male patients was significantly lower than that in female patients (t=-2.120,P<0.05). The patients aged ≥55 years showed a significantly higher level of NK cells and significantly lower levels of CD3+ T cells and CD8+T compared with those aged <55 years (z=-2.344, -2.681,t=2.266,P<0.05). The levels of CD3+ T cells, CD4+ T cells, and CD4/CD8 were significantly lower in the patients with maximum tumor diameter >2 cm than in those with maximum tumor dia-meter ≤2 cm (z=2.595, -2.652,t=3.861,P<0.05). The level of CD4+ T cells in the M1 group was significantly lower than that in the M0 group (t=4.035,P<0.05). Conclusion The cellular immune status is associated with the clinicopathological features of patients with DTC after surgery and before 131I therapy, with significantly decreased levels of peripheral blood CD4+ T cells for males, maximum tumor diameter >2 cm, and M1 stage. Monitoring lymphocyte subsets can help guide interventions for patients from the immune perspective

Shape memory polyurethane with polydopamine-coated nanosheets: Simultaneous enhancement of recovery stress and strain recovery ratio and the underlying mechanisms

Two different sizes of polydopamine-coated layered double hydroxides (D-LDHs) are incorporated into polycaprolactone-based polyurethane (PU) to enhance the mechanical and shape memory properties of the PU. The results show that D-LDH interacts strongly with hard segments and hence enhancing phase separation between hard and soft segments. It is found that the tensile moduli of the PU/D-LDH nanocomposites are much higher than that of neat PU at 60 oC. In comparison with neat PU, the nanocomposite with 2 wt% of small D-LDH exhibits a 60% increase in recovery stress while shape fixity and strain recovery ratio are also improved simultaneously. This is because at low filler loading, most small D-LDH nanosheets interact with hard domains and they are not large enough to connect neighbor hard domains. They can hence reinforce the hard domains without sacrificing the elasticity of the system. Two-dimensional X-ray diffraction studies indicate that most small D-LDH nanosheets are able to rotate back from aligned state to original random state in shape recovery process, justifying the improved strain recovery ratio.ASTAR (Agency for Sci., Tech. and Research, S’pore)Accepted versio