Knowledge Based Template Machine Translation In Low-Resource Setting

Incorporating tagging into neural machine translation (NMT) systems has shown promising results in helping translate rare words such as named entities (NE). However, translating NE in low-resource setting remains a challenge. In this work, we investigate the effect of using tags and NE hypernyms from knowledge graphs (KGs) in parallel corpus in different levels of resource conditions. We find the tag-and-copy mechanism (tag the NEs in the source sentence and copy them to the target sentence) improves translation in high-resource settings only. Introducing copying also results in polarizing effects in translating different parts-of-speech (POS). Interestingly, we find that copy accuracy for hypernyms is consistently higher than that of entities. As a way of avoiding "hard" copying and utilizing hypernym in bootstrapping rare entities, we introduced a "soft" tagging mechanism and found consistent improvement in high and low-resource settings

AugCSE: contrastive sentence embedding with diverse augmentations

Data augmentation techniques have been proven useful in many applications in NLP fields. Most augmentations are task-specific, and cannot be used as a general-purpose tool. In our work, we present AugCSE, a unified framework to utilize diverse sets of data augmentations to achieve a better, general-purpose, sentence embedding model. Building upon the latest sentence embedding models, our approach uses a simple antagonistic discriminator that differentiates the augmentation types. With the finetuning objective borrowed from domain adaptation, we show that diverse augmentations, which often lead to conflicting contrastive signals, can be tamed to produce a better and more robust sentence representation. Our methods achieve state-of-the-art results on downstream transfer tasks and perform competitively on semantic textual similarity tasks, using only unsupervised data.000000000000000000000000000000000000000000000000000000010241 - University of California, Berkeleyhttps://aclanthology.org/2022.aacl-main.30/First author draf

Explain-then-Translate: An Analysis on Improving Program Translation with Self-generated Explanations

This work explores the use of self-generated natural language explanations as an intermediate step for code-to-code translation with language models. Across three types of explanations and 19 programming languages constructed from the MultiPL-E dataset, we find the explanations to be particularly effective in the zero-shot case, improving performance by 12% on average. Improvements with natural language explanations are particularly pronounced on difficult programs. We release our dataset, code, and canonical solutions in all 19 languages.Comment: 9 pages, 4 figures, 5 tables, 48 pages total. To be published in EMNLP Findings 202

Expanded genetic screening in Caenorhabditis elegans identifies new regulators and an inhibitory role for NAD+ in axon regeneration.

The mechanisms underlying axon regeneration in mature neurons are relevant to the understanding of normal nervous system maintenance and for developing therapeutic strategies for injury. Here, we report novel pathways in axon regeneration, identified by extending our previous function-based screen using the C. elegans mechanosensory neuron axotomy model. We identify an unexpected role of the nicotinamide adenine dinucleotide (NAD+) synthesizing enzyme, NMAT-2/NMNAT, in axon regeneration. NMAT-2 inhibits axon regrowth via cell-autonomous and non-autonomous mechanisms. NMAT-2 enzymatic activity is required to repress regrowth. Further, we find differential requirements for proteins in membrane contact site, components and regulators of the extracellular matrix, membrane trafficking, microtubule and actin cytoskeleton, the conserved Kelch-domain protein IVNS-1, and the orphan transporter MFSD-6 in axon regrowth. Identification of these new pathways expands our understanding of the molecular basis of axonal injury response and regeneration

Are Proselfs More Deceptive and Hypocritical? Social Image Concerns in Appearing Fair

Deception varies across individuals and social contexts. The present research explored how individual difference measured by social value orientations, and situations, affect deception in moral hypocrisy. In two experiments, participants made allocations between themselves and recipients with an opportunity to deceive recipients where recipients cannot reject their allocations. Experiment 1 demonstrated that proselfs were more deceptive and hypocritical than prosocials by lying to be apparently fair, especially when deception was unrevealed. Experiment 2 showed that proselfs were more concerned about social image in deception in moral hypocrisy than prosocials were. They decreased apparent fairness when deception was revealed and evaluated by a third-party reviewer and increased it when deception was evaluated but unrevealed. These results show that prosocials and proselfs differed in pursuing deception and moral hypocrisy social goals and provide implications for decreasing deception and moral hypocrisy

An anoikis-related gene signature for prediction of the prognosis in prostate cancer

PurposeThis study presents a novel approach to predict postoperative biochemical recurrence (BCR) in prostate cancer (PCa) patients which involves constructing a signature based on anoikis-related genes (ARGs).MethodsIn this study, we utilised data from TCGA-PARD and GEO databases to identify specific ARGs in prostate cancer. We established a signature of these ARGs using Cox regression analysis and evaluated their clinical predictive efficacy and immune-related status through various methods such as Kaplan-Meier survival analysis, subject work characteristics analysis, and CIBERSORT method. Our findings suggest that these ARGs may have potential as biomarkers for prostate cancer prognosis and treatment. To investigate the biological pathways of genes associated with anoikis, we utilised GSVA, GO, and KEGG. The expression of ARGs was confirmed by the HPA database. Furthermore, we conducted PPI analysis to identify the core network of ARGs in PCa.ResultsBased on analysis of the TCGA database, a set of eight ARGs were identified as prognostic signature genes for prostate cancer. The reliability and validity of this signature were well verified in both the TCGA and GEO codifications. Using this signature, patients were classified into two groups based on their risk for developing BCR. There was a significant difference in BCR-free time between the high and low risk groups (P < 0.05).This signature serves as a dependable and unbiased prognostic factor for predicting biochemical recurrence (BCR) in prostate cancer (PCa) patients. It outperforms clinicopathological characteristics in terms of accuracy and reliability. PLK1 may play a potential regulatory role as a core gene in the development of prostate cancer.ConclusionThis signature suggests the potential role of ARGs in the development and progression of PCa and can effectively predict the risk of BCR in PCa patients after surgery. It also provides a basis for further research into the mechanism of ARGs in PCa and for the clinical management of patients with PCa

Expanded Genetic Screening in \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e Identifies New Regulators and an Inhibitory Role for NAD\u3csup\u3e+\u3c/sup\u3e in Axon Regeneration

The mechanisms underlying axon regeneration in mature neurons are relevant to the understanding of normal nervous system maintenance and for developing therapeutic strategies for injury. Here, we report novel pathways in axon regeneration, identified by extending our previous function-based screen using the C. elegans mechanosensory neuron axotomy model. We identify an unexpected role of the nicotinamide adenine dinucleotide (NAD+) synthesizing enzyme, NMAT-2/NMNAT, in axon regeneration. NMAT-2 inhibits axon regrowth via cell-autonomous and non-autonomous mechanisms. NMAT-2 enzymatic activity is required to repress regrowth. Further, we find differential requirements for proteins in membrane contact site, components and regulators of the extracellular matrix, membrane trafficking, microtubule and actin cytoskeleton, the conserved Kelch-domain protein IVNS-1, and the orphan transporter MFSD-6 in axon regrowth. Identification of these new pathways expands our understanding of the molecular basis of axonal injury response and regeneration

Evaluation of the IP-10 mRNA release assay for diagnosis of TB in HIV-infected individuals

HIV-infected individuals are susceptible to Mycobacterium tuberculosis (M.tb) infection and are at high risk of developing active tuberculosis (TB). Interferon-gamma release assays (IGRAs) are auxiliary tools in the diagnosis of TB. However, the performance of IGRAs in HIV-infected individuals is suboptimal, which limits clinical application. Interferon-inducible protein 10 (IP-10) is an alternative biomarker for identifying M.tb infection due to its high expression after stimulation with M.tb antigens. However, whether IP-10 mRNA constitutes a target for the diagnosis of TB in HIV-infected individuals is unknown. Thus, we prospectively enrolled HIV-infected patients with suspected active TB from five hospitals between May 2021 and May 2022, and performed the IGRA test (QFT-GIT) alongside the IP-10 mRNA release assay on peripheral blood. Of the 216 participants, 152 TB patients and 48 non-TB patients with a conclusive diagnosis were included in the final analysis. The number of indeterminate results of IP-10 mRNA release assay (13/200, 6.5%) was significantly lower than that of the QFT-GIT test (42/200, 21.0%) (P = 0.000026). IP-10 mRNA release assay had a sensitivity of 65.3% (95%CI 55.9% – 73.8%) and a specificity of 74.2% (95%CI 55.4% – 88.1%), respectively; while the QFT-GIT test had a sensitivity of 43.2% (95%CI 34.1% – 52.7%) and a specificity of 87.1% (95%CI 70.2% – 96.4%), respectively. The sensitivity of the IP-10 mRNA release assay was significantly higher than that of QFT-GIT test (P = 0.00062), while no significant difference was detected between the specificities of these two tests (P = 0.198). The IP-10 mRNA release assay showed a lower dependence on CD4+ T cells than that of QFT-GIT test. This was evidenced by the fact that the QFT-GIT test had a higher number of indeterminate results and a lower sensitivity when the CD4+ T cells counts were decreased (P < 0.05), while no significant difference in the number of indeterminate results and sensitivity were observed for the IP-10 mRNA release assay among HIV-infected individuals with varied CD4+T cells counts (P > 0.05). Therefore, our study suggested that M.tb specific IP-10 mRNA is a better biomarker for diagnosis of TB in HIV-infected individuals

Myeloid Cell Hypoxia-Inducible Factors Promote Resolution of Inflammation in Experimental Colitis

Colonic tissues in Inflammatory Bowel Disease (IBD) patients exhibit oxygen deprivation and activation of hypoxia-inducible factor 1α and 2α (HIF-1α and HIF-2α), which mediate cellular adaptation to hypoxic stress. Notably, macrophages and neutrophils accumulate preferentially in hypoxic regions of the inflamed colon, suggesting that myeloid cell functions in colitis are HIF-dependent. By depleting ARNT (the obligate heterodimeric binding partner for both HIFα subunits) in a murine model, we demonstrate here that myeloid HIF signaling promotes the resolution of acute colitis. Specifically, myeloid pan-HIF deficiency exacerbates infiltration of pro-inflammatory neutrophils and Ly6C+ monocytic cells into diseased tissue. Myeloid HIF ablation also hinders macrophage functional conversion to a protective, pro-resolving phenotype, and elevates gut serum amyloid A levels during the resolution phase of colitis. Therefore, myeloid cell HIF signaling is required for efficient resolution of inflammatory damage in colitis, implicating serum amyloid A in this process