Miracle-dz/UniFAR-FTUs huggingface dataset:
A Unified Generative Retriever for Knowledge-Intensive Language Tasks via Prompt Learning

Knowledge-intensive language tasks (KILTs) benefit from retrieving high-quality relevant contexts from large external knowledge corpora. Learning task-specific retrievers that return relevant contexts at an appropriate level of semantic granularity, such as a document retriever, passage retriever, sentence retriever, and entity retriever, may help to achieve better performance on the end-to-end task. But a task-specific retriever usually has poor generalization ability to new domains and tasks, and it may be costly to deploy a variety of specialised retrievers in practice. We propose a unified generative retriever (UGR) that combines task-specific effectiveness with robust performance over different retrieval tasks in KILTs. To achieve this goal, we make two major contributions: (i) To unify different retrieval tasks into a single generative form, we introduce an n-gram-based identifier for relevant contexts at different levels of granularity in KILTs. And (ii) to address different retrieval tasks with a single model, we employ a prompt learning strategy and investigate three methods to design prompt tokens for each task. In this way, the proposed UGR model can not only share common knowledge across tasks for better generalization, but also perform different retrieval tasks effectively by distinguishing task-specific characteristics. We train UGR on a heterogeneous set of retrieval corpora with well-designed prompts in a supervised and multi-task fashion. Experimental results on the KILT benchmark demonstrate the effectiveness of UGR on in-domain datasets, out-of-domain datasets, and unseen tasks.
CED: Catalog Extraction from Documents

Sentence-by-sentence information extraction from long documents is an exhausting and error-prone task. As the indicator of document skeleton, catalogs naturally chunk documents into segments and provide informative cascade semantics, which can help to reduce the search space. Despite their usefulness, catalogs are hard to be extracted without the assist from external knowledge. For documents that adhere to a specific template, regular expressions are practical to extract catalogs. However, handcrafted heuristics are not applicable when processing documents from different sources with diverse formats. To address this problem, we build a large manually annotated corpus, which is the first dataset for the Catalog Extraction from Documents (CED) task. Based on this corpus, we propose a transition-based framework for parsing documents into catalog trees. The experimental results demonstrate that our proposed method outperforms baseline systems and shows a good ability to transfer. We believe the CED task could fill the gap between raw text segments and information extraction tasks on extremely long documents. Data and code are available at \url{https://github.com/Spico197/CatalogExtraction}
Employing Socially Assistive Robots in Elderly Care (longer version)

Recently, it has been considering robotics to face world population aging. According to the WHO, in 2050 there will be about 2.1 billion people over 60 years old worldwide causing a persistent growing need of assistance and a shortage of manpower for delivering congruous assistance. Therefore, seniors' QoL is continuously threatened. Socially Assistive Robotics proposes itself as a solution. To improve SARs acceptability, it is necessary to tailor the system's characteristics with respect to the target needs and issues through the analysis of previous and current studies in the HRI field. Through the examination of the state of the art of social robotics in elderly care, past case studies and paper research about SARs' efficiency, it has been proposed two potential solution examples for two different scenarios, applying two different SARs: Pepper and Nao robots.
First-principles Prediction of Potential Candidate Materials MCu$_3$X$_4$ (M = V, Nb, Ta; X = S, Se, Te) for Neuromorphic Computing

Inspired by the neuro-synaptic frameworks in the human brain, neuromorphic computing is expected to overcome the bottleneck of traditional von-Neumann architecture and be used in artificial intelligence. Here, we predict a class of potential candidate materials, MCu$_3$X$_4$ (M = V, Nb, Ta; X = S, Se, Te), for neuromorphic computing applications through first-principles calculations based on density functional theory. We find that when MCu$_3$X$_4$ are inserted with Li atom, the systems would transform from semiconductors to metals due to the considerable electron filling [~0.8 electrons per formula unit (f.u.)] and still maintain well structural stability. Meanwhile, the inserted Li atom also has a low diffusion barrier (~0.6 eV/f.u.), which ensures the feasibility to control the insertion/extraction of Li by gate voltage. These results establish that the system can achieve the reversible switching between two stable memory states, i.e., high/low resistance state, indicating that it could potentially be used to design synaptic transistor to enable neuromorphic computing. Our work provides inspiration for advancing the search of candidate materials related to neuromorphic computing from the perspective of theoretical calculations.
Concentric Reversible Visual Field Loss, Nyctalopia, and Dyschromatopsia with Ezetimibe Therapy

This is a case of ezetimibe-induced concentric field loss, dyschromatopsia, and nyctalopia in a patient with no prior history of retinal dystrophy or drug hypersensitivity. A 55-year-old Caucasian woman presents with a 1-year history of increasing concentric visual field loss, nyctalopia, photophobia, and colour vision impairment. These symptoms correlated with the commencement of ezetimibe therapy 10 mg daily for hypercholesterolaemia. She demonstrated repeatable bilateral visual field constriction on 30-2 Humphrey visual filed testing and colour vision impairment on Ishihara plates (OD: 1/17, OS: 1/17). Biochemical and radiological screening for carcinoma-associated retinopathy was unremarkable. A working diagnosis of drug-induced rod-cone dysfunction was made. Her visual symptoms and field changes completely resolved 3 months after cessation of ezetimibe therapy. This case suggests that ezetimibe is a potential cause of rod-cone dysfunction and should be considered as a differential in patients with new unexplained visual symptoms.
ANALYSIS AND NUMERICAL APPROXIMATIONS OF EQUATIONS OF NONLINEAR POROELASTICITY

The equations of quasi-static poroelasticity which model flow through elastic porous media are considered. It is assumed that the hydraulic conductivity depends nonlinearly on the displacement (the dilatation) of the medium. The existence of a weak solution is proved using the modified Rothe's method. Numerical approximations of solutions by the finite element method are considered. Error estimates are obtained and numerical experiments are conducted to illustrate the theoretical results, and the efficiency and accuracy of the numerical method.
Multi-omics analysis reveals the molecular mechanisms underlying virulence in Rhizoctonia and jasmonic acid-mediated resistance in Tartary buckwheat (Fagopyrum tataricum).

Rhizoctonia solani is a devastating soil-borne pathogen that seriously threatens the cultivation of economically important crops. Multiple strains with a very broad host range have been identified, but only one (AG1-IA, which causes rice sheath blight disease) has been examined in detail. Here, we analyzed AG4-HGI 3 originally isolated from Tartary buckwheat (Fagopyrum tataricum), but with a host range comparable to AG1-IA. Genome comparison reveals abundant pathogenicity genes in this strain. We used multi-omics approaches to improve the efficiency of screening for disease resistance genes. Transcriptomes of the plant-fungi interaction identified differentially expressed genes associated with virulence in Rhizoctonia and resistance in Tartary buckwheat. Integration with jasmonate-mediated transcriptome and metabolome changes revealed a negative regulator of jasmonate signaling, cytochrome P450 (FtCYP94C1), as increasing disease resistance probably via accumulation of resistance-related flavonoids. The integration of resistance data for 320 Tartary buckwheat accessions identified a gene homologous to aspartic proteinase (FtASP), with peak expression following R. solani inoculation. FtASP exhibits no proteinase activity but functions as an antibacterial peptide that slows fungal growth. This work reveals a potential mechanism behind pathogen virulence and host resistance, which should accelerate the molecular breeding of resistant varieties in economically essential crops.
The start of frozen dates over northern permafrost regions with the changing climate

The soil freeze–thaw cycle in the permafrost regions has a significant impact on regional surface energy and water balance. Although increasing efforts have been made to understand the responses of spring thawing to climate change, the mechanisms controlling the global interannual variability of the start date of permafrost frozen (SOF) remain unclear. Using long‐term SOF from the combinations of multiple satellite microwave sensors between 1979 and 2020, and analytical techniques, including partial correlation, ridge regression, path analysis, and machine learning, we explored the responses of SOF to multiple climate change factors, including warming (surface and air temperature), start date of permafrost thawing (SOT), soil properties (soil temperature and volume of water), and the snow depth water equivalent (SDWE). Overall, climate warming exhibited the maximum control on SOF, but SOT in spring was also an important driver of SOF variability; among the 65.9% significant SOT and SOF correlations, 79.3% were positive, indicating an overall earlier thawing would contribute to an earlier frozen in winter. The machine learning analysis also suggested that apart from warming, SOT ranked as the second most important determinant of SOF. Therefore, we identified the mechanism responsible for the SOT–SOF relationship using the SEM analysis, which revealed that soil temperature change exhibited the maximum effect on this relationship, irrespective of the permafrost type. Finally, we analyzed the temporal changes in these responses using the moving window approach and found increased effect of soil warming on SOF. In conclusion, these results provide important insights into understanding and predicting SOF variations with future climate change.
Optimization of partial association rules relative to number of misclassifications

In the paper, an optimization of partial association rules relative to number of misclassifications is presented. The aims of proposed optimization are: (i) construction of rules with small number of misclassifications, what is important from the point of view of construction of classifiers, (ii) decreasing the number of rules, what is important from the point of view of knowledge representation. The paper contains experimental results for data sets from UCI Machine Learning Repository.
A Primer on Interoception and its Importance in Psychiatry

Interoception is the perception of signals from inside the body. It plays a significant role in the nervous, cardiovascular, respiratory, gastrointestinal, genitourinary, and endocrine systems. It is also closely related to the autonomic nervous system and inflammatory pathways and plays a significant role in our optimal functioning. Recently, interoception has gained more attention in neuropsychiatric research. Anatomical and physiological aspects of interoception like relevant brain areas, the role of the vagus nerve, and the autonomic nervous system are gradually being understood. Different facets of interoception like interoceptive attention, detection, magnitude, discrimination, accuracy, awareness, and appraisal have been proposed and their assessments and importance are being evaluated. Further, interoception is often dysregulated or abnormal in psychiatric disorders. It has been implicated in the psychopathology, etiopathogenesis, clinical features and treatment of mood, anxiety, psychotic, personality and addiction-related disorders. This narrative review attempts to provide a nuanced understanding of the pathway(s), components, functions, assessments, and problems of interoception and will help us to detect its disturbances and evaluate its impact on psychiatric disorders, leading to a better perspective and management. This will also advance interoception-related research.
A perspective on Notch signalling in progression and arrhythmogenesis in familial hypertrophic and dilated cardiomyopathies

In this perspective, we discussed emerging data indicating a role for Notch signalling in inherited disorders of the heart failure with focus on hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) linked to variants of genes encoding mutant proteins of the sarcomere. We recently reported an upregulation of elements in the Notch signalling cascade in cardiomyocytes derived from human inducible pluripotent stem cells expressing a TNNT2 variant encoding cardiac troponin T (cTnT-I79N+/−), which induces hypertrophy, remodelling, abnormalities in excitation–contraction coupling and electrical instabilities (Shafaattalab S et al. 2021 Front. Cell Dev. Biol. 9, 787581. (doi:10.3389/fcell.2021.787581)). Our search of the literature revealed the novelty of this finding and stimulated us to discuss potential connections between the Notch signalling pathway and familial cardiomyopathies. Our considerations focused on the potential role of these interactions in arrhythmias, microvascular ischaemia, and fibrosis. This finding underscored a need to consider the role of Notch signalling in familial cardiomyopathies which are trigged by sarcomere mutations engaging mechano-signalling pathways for which there is evidence of a role for Notch signalling with crosstalk with Hippo signalling. Our discussion included a role for both cardiac myocytes and non-cardiac myocytes in progression of HCM and DCM. This article is part of the theme issue ‘The heartbeat: its molecular basis and physiological mechanisms’.
Feedback contributions to excitation–contraction coupling in native functioning striated muscle

Skeletal and cardiac muscle excitation–contraction coupling commences with Nav1.4/Nav1.5-mediated, surface and transverse (T-) tubular, action potential generation. This initiates feedforward, allosteric or Ca2+-mediated, T-sarcoplasmic reticular (SR) junctional, voltage sensor-Cav1.1/Cav1.2 and ryanodine receptor-RyR1/RyR2 interaction. We review recent structural, physiological and translational studies on possible feedback actions of the resulting SR Ca2+ release on Nav1.4/Nav1.5 function in native muscle. Finite-element modelling predicted potentially regulatory T-SR junctional [Ca2+]TSR domains. Nav1.4/Nav1.5, III-IV linker and C-terminal domain structures included Ca2+ and/or calmodulin-binding sites whose mutations corresponded to specific clinical conditions. Loose-patch-clamped native murine skeletal muscle fibres and cardiomyocytes showed reduced Na+ currents (INa) following SR Ca2+ release induced by the Epac and direct RyR1/RyR2 activators, 8-(4-chlorophenylthio)adenosine-3′,5′-cyclic monophosphate and caffeine, abrogated by the RyR inhibitor dantrolene. Conversely, dantrolene and the Ca2+-ATPase inhibitor cyclopiazonic acid increased INa. Experimental, catecholaminergic polymorphic ventricular tachycardic RyR2-P2328S and metabolically deficient Pgc1β−/− cardiomyocytes also showed reduced INa accompanying [Ca2+]i abnormalities rescued by dantrolene- and flecainide-mediated RyR block. Finally, hydroxychloroquine challenge implicated action potential (AP) prolongation in slowing AP conduction through modifying Ca2+ transients. The corresponding tissue/organ preparations each showed pro-arrhythmic, slowed AP upstrokes and conduction velocities. We finally extend discussion of possible Ca2+-mediated effects to further, Ca2+, K+ and Cl−, channel types. This article is part of the theme issue ‘The heartbeat: its molecular basis and physiological mechanisms’.
Pro-arrhythmic effects of gain-of-function potassium channel mutations in the short QT syndrome

The congenital short QT syndrome (SQTS) is a rare condition characterized by abbreviated rate-corrected QT (QTc) intervals on the electrocardiogram and by increased susceptibility to both atrial and ventricular arrhythmias and sudden death. Although mutations to multiple genes have been implicated in the SQTS, evidence of causality is particularly strong for the first three (SQT1−3) variants: these result from gain-of-function mutations in genes that encode K+ channel subunits responsible, respectively, for the IKr, IKs and IK1 cardiac potassium currents. This article reviews evidence for the impact of SQT1-3 missense potassium channel gene mutations on the electrophysiological properties of IKr, IKs and IK1 and of the links between these changes and arrhythmia susceptibility. Data from experimental and simulation studies and future directions for research in this field are considered. This article is part of the theme issue ‘The heartbeat: its molecular basis and physiological mechanisms’.
Human leukocyte antigen F-associated transcript 10 regulates the IKs potassium channel by competing for Kv7.1 ubiquitination

The protein expression and function changes from the slow-delayed rectifying K+ current, IKs, are tightly associated with ventricular cardiac arrhythmias. Human leukocyte antigen F-associated transcript 10 (FAT10), a member of the ubiquitin-like-modifier family, exerts a protective effect against myocardial ischaemia. However, whether or how FAT10 influences the function of IKs remains unclear. Here, human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and Fat10 knockout HEK293 (Fat10−/−) cells through CRISPR-Cas9 technology were used to evaluate the novel modulation of FAT10 in IKs function. Patch-clamp studies showed that the overexpression of FAT10 significantly enhanced the current density of IKs both in hiPSC-CMs and HEK293-Fat10−/− cells. In addition, a shortened action potential duration (APD) was seen from hiPSC-CMs transfected with the ad-Fat10 virus. Then, a series of molecular approaches from neonatal rat cardiomyocytes, H9C2 cells and HEK293 cells were used to determine the regulatory mechanism of FAT10 in IKs. First, western blot assays indicated that the expression of Kv7.1, the alpha-subunit of IKs, was increased when FAT10 was overexpressed. Furthermore, immunofluorescence and co-immunoprecipitation assays demonstrated that FAT10 could interact with Kv7.1. Notably, FAT10 impedes Kv7.1 ubiquitination and degradation, thereby stabilizing its expression. Finally, a hypoxia model of hiPSC-CMs was established, and the overexpression of FAT10 showed a protective effect against hypoxia-induced decreases in the current density of IKs. Taken together, these findings revealed a novel role of FAT10 in the regulation of the IKs potassium channel by competing for Kv7.1 ubiquitination, which provides a new electrophysiological insight that FAT10 could modulate Kv7.1. This article is part of the theme issue ‘The heartbeat: its molecular basis and physiological mechanisms’.
AGR2: a secreted protein worthy of attention in diagnosis and treatment of breast cancer

AGR2 is a secreted protein widely existing in breast. In precancerous lesions, primary tumors and metastatic tumors, the expression of AGR2 is increased, which has aroused our interest. This review introduces the gene and protein structure of AGR2. Its endoplasmic reticulum retention sequence, protein disulfide isomerase active site and multiple protein binding sequences endow AGR2 with diverse functions inside and outside breast cancer cells. This review also enumerates the role of AGR2 in the progress and prognosis of breast cancer, and emphasizes that AGR2 can be a promising biomarker and a target for immunotherapy of breast cancer, providing new ideas for early diagnosis and treatment of breast cancer.
The survival analysis of rifampicin/multidrug-resistant tuberculosis patients based on the levels of inflammatory biomarkers: a retrospective cohort study

Purpose The development of tuberculosis and inflammatory status are closely related. The aim of this study was to investigate the prognostic value of inflammatory biomarkers in patients with rifampicin/multidrug-resistant tuberculosis (RR/MDR-TB). Patients and methods This study recruited 504 patients with RR/MDR-TB from Wuhan Jinyintan Hospital. A total of 348 RR/MDR patients from January 2017 to December 2019 were defined as training set, the rest of patients as validation set. The patients were divided into three-risk degrees according to the levels of inflammatory biomarkers (median, 85th percentile). Kaplan-Meier curve and log-rank test were used to assess survival differences among the groups. Cox proportion risk regression was used to identify risk factors for RR/MDR-TB mortality. Results In training set, cox proportion risk regression analysis showed that high age (≥60 years) [OR (95%CI):1.053(1.03188-1.077)], smoking [OR (95%CI):2.206(1.191-4.085)], and bronchiectasia [OR (95%CI):2.867(1.548-5.311)] were prognostic factors for RR/MDR-TB patients. In addition, lower survival rates were observed in high CAR group [OR (95%CI):1.464(1.275-1.681)], high CPR group[OR (95%CI):1.268(1.101-1.459)], high CLR group[OR (95%CI):1.004(1.002-1.005)], high NLR group[OR (95%CI):1.103(1.069-1.139)], high PLR group[OR (95%CI):1.003(1.002-1.004)], and high MLR group[OR (95%CI):3.471(2.188-5.508)]. Furthermore, AUCs of age, smoking, bronchiectasia, CAR, CPR, CLR, NLR, PLR, and MLR for predicting mortality in RR/MDR-TB patients were 0.697(95%CI:0.618-0.775), 0.603(95%CI:0.512-0.695), 0.629(95%CI:0.538-0.721), 0.748(95%CI:0.675-0.821, P<0.05), 0.754(95%CI:0.683-0.824, P<0.05), 0.759(95%CI:0.689-0.828, P<0.05), 0.789(95%CI:0.731-0.846, P<0.05), 0.740(95%CI:0.669-0.812, P<0.05), and 0.752(95%CI:0.685-0.819, P<0.05), respectively. Importantly, the AUC of predicting mortality of combination of six inflammatory biomarkers [0.823 (95%CI:0.769-0.876)] is higher than any single inflammatory biomarkers. Additionally, the similar results are also obtained in the validation set. Conclusion Inflammatory biomarkers could predict the survival status of RR/MDR-TB patients. Therefore, more attention should be paid to the level of inflammatory biomarkers in clinical practice.