Continually Updating Generative Retrieval on Dynamic Corpora

Generative retrieval has recently been gaining a lot of attention from the research community for its simplicity, high performance, and the ability to fully leverage the power of deep autoregressive models. However, prior work on generative retrieval has mostly investigated on static benchmarks, while realistic retrieval applications often involve dynamic environments where knowledge is temporal and accumulated over time. In this paper, we introduce a new benchmark called STREAMINGIR, dedicated to quantifying the generalizability of retrieval methods to dynamically changing corpora derived from StreamingQA, that simulates realistic retrieval use cases. On this benchmark, we conduct an in-depth comparative evaluation of bi-encoder and generative retrieval in terms of performance as well as efficiency under varying degree of supervision. Our results suggest that generative retrieval shows (1) detrimental performance when only supervised data is used for fine-tuning, (2) superior performance over bi-encoders when only unsupervised data is available, and (3) lower performance to bi-encoders when both unsupervised and supervised data is used due to catastrophic forgetting; nevertheless, we show that parameter-efficient measures can effectively mitigate the issue and result in competitive performance and efficiency with respect to the bi-encoder baseline. Our results open up a new potential for generative retrieval in practical dynamic environments. Our work will be open-sourced.Comment: Work in progres

A comparative study on experimental and simulation responses of CR-39 to neutron spectra from a 252Cf source

A simulation of the interaction of neutrons emitted from a 252Cf source with a CR-39 detector is presented in this paper. Elastic and inelastic neutron interactions occur with the constituent materials of the CR-39 detector. Inelastic scatterings only consider (n, a) and (n, p) reactions. Fast neutrons tracks are, mainly, produced by recoil particle tracks in the plastic nuclear track detector as a result of the elastic scattering reaction of neutrons with the constituent materials of the solid-state nuclear track detectors, especially hydrogen nuclei. The energy of the neutron, incident position, direction, and type of interaction were sampled by the Monte Carlo method. The energy threshold, critical angle and scattering angle to the detector surface normal were the most important factors considered in our calculations. The energy deposited per neutron mass unit was calculated. The angular response was determined by both Monte Carlo simulation and experimental results. The number of visible proton tracks and energy deposited per neutron per visible track were calculated and simulated. The threshold energy of the recoil proton as a function of the thickness and incident proton angles was measured by the etchable range of protons at scattering angles, along with the shape and diameter of the track. Experimental and simulations result were in good agreement

Spinal cord compression by B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma in a patient seropositive for human immunodeficiency virus: a case report

INTRODUCTION: Although non-Hodgkin’s lymphoma is one of the most common and frequently fatal of the acquired immune deficiency syndrome-defining illnesses, survival has improved significantly since the introduction of antiretroviral therapy. Patients with spinal cord compression resulting from non-Hodgkin’s lymphoma present with clinically acute or rapidly progressive neurologic deficits. The purpose of this case report is to present a case of a patient seropositive for human immunodeficiency virus with spinal cord compression due to B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma. CASE PRESENTATION: A 40-year-old Asian man, who was seropositive for human immunodeficiency virus, presented with progressive neurological deficits. Magnetic resonance images of his thoracic spine showed an epidural mass from T2 to T4, resulting in severe cord compression. Emergent surgical decompression and biopsy were performed, followed by palliative radiation therapy. The pathologic findings showed that the specimen was compatible with B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma. Palliative radiation therapy was performed; however, leptomeningeal seeding and pulmonary embolism led to his death. CONCLUSIONS: When a patient infected with human immunodeficiency virus presents with a rapidly progressive spinal tumor accompanying paraplegia, non-Hodgkin’s lymphoma should be considered, and surgical decompression should be weighed with respect to the patient’s general condition and the subtype/prognosis of the lymphoma

Impacts of Reforestation on Stabilization of Riverine Water Levels in South Korea

We investigate how reforestation contributed to stabilization of riverine water levels in South Korea. For the purpose, we estimate an equation capturing dynamic relationships among rainfall, upstream-area tree stock, and downstream water levels in three river systems of Hongcheon, Mangyeong, and Hyeongsan, using daily observations of precipitation and water levels for the period from 1985 to 2005. Simulation based on estimation results shows that increase in the tree stock in a river basin leads to a significantly suppressed peaking in riverine water levels in response to an abrupt and concentrated rain in the upstream area. For instance, an hour-long concentration of 100mm rain results in 0.7m rise in water level if the volume of growing stock is 1 million m3 , whereas the rise in water level stays below 0.27m with 5 million m3 in the growing-stock volume

A hybrid decision support model to discover informative knowledge in diagnosing acute appendicitis

BACKGROUND: The aim of this study is to develop a simple and reliable hybrid decision support model by combining statistical analysis and decision tree algorithms to ensure high accuracy of early diagnosis in patients with suspected acute appendicitis and to identify useful decision rules. METHODS: We enrolled 326 patients who attended an emergency medical center complaining mainly of acute abdominal pain. Statistical analysis approaches were used as a feature selection process in the design of decision support models, including the Chi-square test, Fisher's exact test, the Mann-Whitney U-test (p < 0.01), and Wald forward logistic regression (entry and removal criteria of 0.01 and 0.05, or 0.05 and 0.10, respectively). The final decision support models were constructed using the C5.0 decision tree algorithm of Clementine 12.0 after pre-processing. RESULTS: Of 55 variables, two subsets were found to be indispensable for early diagnostic knowledge discovery in acute appendicitis. The two subsets were as follows: (1) lymphocytes, urine glucose, total bilirubin, total amylase, chloride, red blood cell, neutrophils, eosinophils, white blood cell, complaints, basophils, glucose, monocytes, activated partial thromboplastin time, urine ketone, and direct bilirubin in the univariate analysis-based model; and (2) neutrophils, complaints, total bilirubin, urine glucose, and lipase in the multivariate analysis-based model. The experimental results showed that the model with univariate analysis (80.2%, 82.4%, 78.3%, 76.8%, 83.5%, and 80.3%) outperformed models using multivariate analysis (71.6%, 69.3%, 73.7%, 69.7%, 73.3%, and 71.5% with entry and removal criteria of 0.01 and 0.05; 73.5%, 66.0%, 80.0%, 74.3%, 72.9%, and 73.0% with entry and removal criteria of 0.05 and 0.10) in terms of accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and area under ROC curve, during a 10-fold cross validation. A statistically significant difference was detected in the pairwise comparison of ROC curves (p < 0.01, 95% CI, 3.13-14.5; p < 0.05, 95% CI, 1.54-13.1). The larger induced decision model was more effective for identifying acute appendicitis in patients with acute abdominal pain, whereas the smaller induced decision tree was less accurate with the test data. CONCLUSIONS: The decision model developed in this study can be applied as an aid in the initial decision making of clinicians to increase vigilance in cases of suspected acute appendicitis

Corrigendum: Secretion of Salmonella Pathogenicity Island 1-Encoded Type III Secretion System Effectors by Outer Membrane Vesicles in Salmonella Enterica Serovar Typhimurium

Outer membrane vesicles (OMVs) are spherical membranous structures released by Gram-negative bacteria. Several bacterial pathogens utilize OMVs as vehicles for the delivery of virulence factors into host cells. Results of our previous study on proteomic analysis revealed that OMVs isolated from Salmonellaenterica serovar Typhimurium had virulence effectors that are known to be translocated by Salmonella pathogenicity island 1 (SPI-1)-encoded type III secretion system (T3SS1) into the host cell. In the present study, immunoblot analysis confirmed the secretion of the six T3SS1 effector proteins, namely SipB and SipC (translocators of T3SS1), and SipA, SopA, SopB, and SopE2 (effectors translocated by T3SS1), by OMVs. Results of proteinase K treatment revealed the localization of these T3SS1 effector proteins on the outer surface of OMVs. SipC and SopE2 were secreted by OMVs independent of the three secretion systems T3SS1, T3SS2, and flagella, signifying OMVs to be an alternative delivery system to T3SSs. T3SS1 effectors SipA, SipC, and SopE2 were internalized into the cytoplasm of the host cell by OMVs independent of cellular Salmonella–host cell contact. In epithelial cells, addition of OMVs harboring T3SS1 effectors stimulated the production of F-actin, thereby complementing the attenuated invasion of ΔsopE2 into host cells. These results suggest that S. Typhimurium might exploit OMVs as a long-distance vehicle to deliver T3SS1 effectors into the cytoplasm of the host cell independent of bacteria–host cell interaction

Secretion of Salmonella Pathogenicity Island 1-Encoded Type III Secretion System Effectors by Outer Membrane Vesicles in Salmonella enterica Serovar Typhimurium

Outer membrane vesicles (OMVs) are spherical membranous structures released by Gram-negative bacteria. Several bacterial pathogens utilize OMVs as vehicles for the delivery of virulence factors into host cells. Results of our previous study on proteomic analysis revealed that OMVs isolated from Salmonellaenterica serovar Typhimurium had virulence effectors that are known to be translocated by Salmonella pathogenicity island 1 (SPI-1)-encoded type III secretion system (T3SS1) into the host cell. In the present study, immunoblot analysis confirmed the secretion of the six T3SS1 effector proteins, namely SipB and SipC (translocators of T3SS1), and SipA, SopA, SopB, and SopE2 (effectors translocated by T3SS1), by OMVs. Results of proteinase K treatment revealed the localization of these T3SS1 effector proteins on the outer surface of OMVs. SipC and SopE2 were secreted by OMVs independent of the three secretion systems T3SS1, T3SS2, and flagella, signifying OMVs to be an alternative delivery system to T3SSs. T3SS1 effectors SipA, SipC, and SopE2 were internalized into the cytoplasm of the host cell by OMVs independent of cellular Salmonella–host cell contact. In epithelial cells, addition of OMVs harboring T3SS1 effectors stimulated the production of F-actin, thereby complementing the attenuated invasion of ΔsopE2 into host cells. These results suggest that S. Typhimurium might exploit OMVs as a long-distance vehicle to deliver T3SS1 effectors into the cytoplasm of the host cell independent of bacteria–host cell interaction

Oxygen Partial Pressure during Pulsed Laser Deposition: Deterministic Role on Thermodynamic Stability of Atomic Termination Sequence at SrRuO3/BaTiO3 Interface

With recent trends on miniaturizing oxide-based devices, the need for atomic-scale control of surface/interface structures by pulsed laser deposition (PLD) has increased. In particular, realizing uniform atomic termination at the surface/interface is highly desirable. However, a lack of understanding on the surface formation mechanism in PLD has limited a deliberate control of surface/interface atomic stacking sequences. Here, taking the prototypical SrRuO3/BaTiO3/SrRuO3 (SRO/BTO/SRO) heterostructure as a model system, we investigated the formation of different interfacial termination sequences (BaO-RuO2 or TiO2-SrO) with oxygen partial pressure (PO2) during PLD. We found that a uniform SrO-TiO2 termination sequence at the SRO/BTO interface can be achieved by lowering the PO2 to 5 mTorr, regardless of the total background gas pressure (Ptotal), growth mode, or growth rate. Our results indicate that the thermodynamic stability of the BTO surface at the low-energy kinetics stage of PLD can play an important role in surface/interface termination formation. This work paves the way for realizing termination engineering in functional oxide heterostructures.Comment: 27 pages, 6 figures, Supporting Informatio