Zero-shot Domain-sensitive Speech Recognition with Prompt-conditioning Fine-tuning

In this work, we propose a method to create domain-sensitive speech recognition models that utilize textual domain information by conditioning its generation on a given text prompt. This is accomplished by fine-tuning a pre-trained, end-to-end model (Whisper) to learn from demonstrations with prompt examples. We show that this ability can be generalized to different domains and even various prompt contexts, with our model gaining a Word Error Rate (WER) reduction of up to 33% on unseen datasets from various domains, such as medical conversation, air traffic control communication, and financial meetings. Considering the limited availability of audio-transcript pair data, we further extend our method to text-only fine-tuning to achieve domain sensitivity as well as domain adaptation. We demonstrate that our text-only fine-tuned model can also attend to various prompt contexts, with the model reaching the most WER reduction of 29% on the medical conversation dataset.Comment: F-T Liao and Y-C Chan contributed equall

Cloning, purification, and functional characterization of Carocin S2, a ribonuclease bacteriocin produced by Pectobacterium carotovorum

<p>Abstract</p> <p>Background</p> <p>Most isolates of <it>Pectobacterium carotovorum subsp. carotovorum </it>(Pcc) produce bacteriocins. In this study, we have determined that Pcc strain F-rif-18 has a chromosomal gene encoding the low-molecular-weight bacteriocin, Carocin S2, and that this bacteriocin inhibits the growth of a closely related strain. Carocin S2 is inducible by ultraviolet radiation but not by mutagenic agents such as mitomycin C.</p> <p>Results</p> <p>A carocin S2-defective mutant, TF1-2, was obtained by Tn5 insertional mutagenesis using F-rif-18. A 5706-bp DNA fragment was detected by Southern blotting, selected from a genomic DNA library, and cloned to the vector, pMS2KI. Two adjacent complete open reading frames within pMS2KI were sequenced, characterized, and identified as caroS2K and caroS2I, which respectively encode the killing protein and immunity protein. Notably, carocin S2 could be expressed not only in the mutant TF1-2 but also in <it>Escherichia coli </it>DH5α after entry of the plasmid pMS2KI. Furthermore, the C-terminal domain of CaroS2K was homologous to the nuclease domains of colicin D and klebicin D. Moreover, SDS-PAGE analysis showed that the relative mass of CaroS2K was 85 kDa and that of CaroS2I was 10 kDa.</p> <p>Conclusion</p> <p>This study shown that another nuclease type of bacteriocin was found in <it>Pectobacterium carotovorum</it>. This new type of bacteriocin, Carocin S2, has the ribonuclease activity of CaroS2K and the immunity protein activity of CaroS2I.</p

Acute Kidney Injury Biomarkers for Patients in a Coronary Care Unit: A Prospective Cohort Study

Background: Renal dysfunction is an established predictor of all-cause mortality in intensive care units. This study analyzed the outcomes of coronary care unit (CCU) patients and evaluated several biomarkers of acute kidney injury (AKI), including neutrophil gelatinase-associated lipocalin (NGAL), interleukin-18 (IL-18) and cystatin C (CysC) on the first day of CCU admission. Methodology/Principal Findings: Serum and urinary samples collected from 150 patients in the coronary care unit of a tertiary care university hospital between September 2009 and August 2010 were tested for NGAL, IL-18 and CysC. Prospective demographic, clinical and laboratory data were evaluated as predictors of survival in this patient group. The most common cause of CCU admission was acute myocardial infarction (80%). According to Acute Kidney Injury Network criteria, 28.7 % (43/150) of CCU patients had AKI of varying severity. Cumulative survival rates at 6-month follow-up following hospital discharge differed significantly (p,0.05) between patients with AKI versus those without AKI. For predicting AKI, serum CysC displayed an excellent areas under the receiver operating characteristic curve (AUROC) (0.89560.031, p,0.001). The overall 180-day survival rate was 88.7 % (133/150). Multiple Cox logistic regression hazard analysis revealed that urinary NGAL, serum IL-18, Acute Physiology, Age and Chronic Health Evaluation II (APACHE II) and sodium on CCU admission day one were independent risk factors for 6-month mortality. In terms of 6-month mortality, urinary NGAL had the best discriminatory power, the best Youden index, and the highest overall correctness of prediction

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Synthesis and Application in Cell Imaging of Acridone Derivatives

Tricyclic acridone derivatives have been extensively developed as antimicrobial, antimalarial, and antitumor drugs due to their broad spectrum of drug design and biological activity. In this study, we developed a surfactant-like acridone scaffold that contained two vinylpyridines and a dodecyl pyridine chain. The acridone scaffold decorated the dodecyl pyridine chain by N-bromosuccinimide reagent. The surfactant-like core scaffold incorporated with 4-vinylpyridines at the 2- and 7-positions via a Heck coupling reaction. Subsequently, the acridone derivatives were methylated onto these pyridine groups. Here we developed two similar acridone derivatives, MedAcd12C and MedAcd12P. The MedAcd12C incorporated two pyridine groups, and MedAcd12P incorporated three pyridine groups. MedAcd12C and MedAcd12P have two identical vinylpyridines and the different anchor tails at the N10 position. Their physicochemical properties, cell compatibility, and photoluminescence were demonstrated. Although both compounds have no fluorescence emission in water solution, MedAcd12P and MedAcd12C significantly appeared with orange light emission in the cellular imaging. We suggested that the surfactant-like scaffold promoted the drugs&rsquo; self-assembly and caused the aggregation-induced emission (AIE) after cellular uptake. This innovative design endowed acridone derivatives with an AIE and traceability for cell imaging

Gene Cloning and Analysis of Low-Molecular-Weight Bacteriocin Secretary Protein of Erwinia carotovora subsp. carotovora

Erwinia. carotovora subsp. carotovora是一種會造成許多植物根莖部腐爛的病原菌。大多作物常因感染此病原菌而失去經濟價值，但是到目前為止仍沒方法可以有效抑制此菌種造成的損害。由於此菌種會生產一至數種細菌素以抑制其他親屬相近的菌種生長，而被當作是一種有效的微生物農藥使用，但其細菌素相關研究仍然十分不足。 TH22-6 是一株被transposon Tn5 阻斷其低分子量細菌素生產相關基因的Erwinia. carotovora subsp. carotovora 野生株H-rif-8-6 的突變株。我們利用TAIL-PCR 的方法增幅並定序transposon Tn5 左右兩端向外延伸的DNA片段。此序列經過美國國家衛生研究院醫學圖書館的資料庫(NCBI)比對胺基酸序列(BLAST)，結果發現在此DNA片段與第三類型分泌系統的蛋白胺基酸序列有相當高的同質性。因此我們認為被Tn5 阻斷的基因為一種類似第三類分泌系統蛋白的基因。根據此比對結果我們推測Erwinia. carotovora subsp. carotovora可能經由類似第三類分泌系統的機制運送低分子量細菌素。 第三類分泌系統主要功能為分泌由病原菌產生的毒性蛋白，目前文獻指出其作用對象為動物或植物細胞。有趣的是在本文，我們卻發現低分子量細菌素可藉由類似第三類型分泌系統的機制分泌並感染其他菌種。希望此結果能幫助我們更加了解Erwinia carotovora subsp. carotovora 產生的低分子量細菌素其分泌系統作用的機制。Erwinia. carotovora subsp. carotovora is a phytopathogenic bacterium responsible for the soft-rot disease of many plants. It will decompose the crops, but there is no efficiently approach to bate the damages caused by the bacterium. Low-molecular-weight bacteriocin is an antibacterial substance which could be produced by Erwinia. carotovora subsp. carotovora, and inhibit the related strain growth. The bacteriocin could be used as effectively biopesticides, but the realtived study is still not enough. TH22-6 is a Transposon Tn5 insertional mutant strain from Erwinia. carotovora subsp. carotovora, it could not generate low-molecular-weight bacteriocin. We used TAIL-PCR method to amplify and analyze the DNA sequence of the insert end from transposon Tn5. The DNA sequence was compared with the BLAST of the National Center for Biotechnology Information server, then the result show that has high homology with the genes of secretary protein in bacterium, especially the type Ⅲ secretion system. According to the comparison, this result suggest the low-molecular- weight bacteriocin may be transport by the type Ⅲ-like secretion system. The function of type Ⅲ secretion system is usually the infection to the animal or the plant cell. In this study, it is interesting to find the relationship between low-molecular-weight bacteriocin and the type Ⅲ-like secretion system. The result may helpfully let we know the mechanism of low-molecular-weight bacteriocin and secretion system in Erwinia. carotovora subsp. carotovora.目次 第一章 緒論 …………………………………….………………………….....1 第二章 利用Transposon Tn5 阻斷E.C.C. 的低分子量細菌素生產相關基因 一. 目的……………………………………………………………..….8 二. 材料與方法……………………………………………………..….8 三. 結果……………………………………………………………….10 第三章 利用TAIL-PCR 的方法增幅並定序被Transposon Tn5阻斷的基因 一. 目的…………………………………………………………….…12 二. 材料與方法……………………………………………………….12 三. 結果……………………………………………………………….15 第四章 Erwinia. carotovora subsp. carotovora 低分子量細菌素分泌蛋白基因(BSP)的選殖 一. 目的…………………………………………………………….…21 二. 材料與方法……………………………………………………….21 三. 結果……………………………………………………………….24 第五章 BSP蛋白基因表現質體的構築與低分子量細菌素恢復實驗 一. 目的…………………………………………………………….…32 二. 材料與方法……………………………………………………….32 三. 結果……………………………………………………………….34 第六章 結論 ………………………………………………………………... 44 附錄………………………………………………………………………………55 參考文獻…………………………………………………………………………6

Plasmon-Enhanced Photodynamic Cancer Therapy by Upconversion Nanoparticles Conjugated with Au Nanorods

Photodynamic therapy (PDT) based on photosensitizers (PSs) constructed with nanomaterials has been widely applied to treat cancer. This therapy is characterized by an improved PS accumulation in tumor regions. However, challenges, such as short penetration depth of light and low extinction coefficient of PSs, limit PDT applications. In this study, a nanocomposite consisting of NaYF₄:Yb/Er upconversion nanoparticles (UCPs) conjugated with gold nanorods (Au NRs) was developed to improve the therapeutic efficiency of PDT. Methylene blue (MB) was embedded in a silica shell for plasmon-enhanced PDT. UCPs served as a light converter from near-infrared (NIR) to visible light to excite MB to generate reactive oxygen species (ROS). Au NRs could effectively enhance upconversion efficiency and ROS content through a localized surface plasmon resonance (SPR) effect. Silica shell thickness was adjusted to investigate the optimized MB loading amount, ROS production capability, and efficient distance for plasmon-enhanced ROS production. The mechanism of plasmon-enhanced PDT was verified by enhancing UC luminescence intensity through the plasmonic field and by increasing the light-harvesting capability and absorption cross section of the system. This process improved the ROS generation by comparing the exchange of Au NRs to Au nanoparticles with different SPR bands. NIR-triggered nanocomposites of UCP@SiO₂:MB-NRs were significantly confirmed by improving ROS generation and further modifying folic acid (FA) to develop an active component targeting OECM-1 oral cancer cells. Consequently, UCP@SiO₂:MB-NRs-FA could highly produce ROS and undergo efficient PDT in vitro and in vivo. The mechanism of PDT treatment by UCP@SiO₂:MB-NRs-FA was evaluated via the cell apoptosis pathway. The proposed process is a promising strategy to enhance ROS production through plasmonic field enhancement and thus achieve high PDT therapeutic efficacy

Aggregation-induced emission enhancement characteristics of naphthalimide derivatives and their applications in cell imaging

Novel naphthalimide derivatives (NIM) with donor-acceptor architecture were successfully constructed and their unique fluorescent properties were investigated. In particular, the fluorescence intensities of 4-methoxystyrene substituted NIM-1 were solvent independent and its quantum yields varied from 0.4 in toluene to 0.52 in MeOH. However, 4-(N,N-diphenylamino) styrene substituted NIM-2 and 4-nitrostyrene substituted NIM-3 exhibited low luminescence in dilute solutions but were efficiently fluorescent under conditions of molecular aggregation. NIM-2 showed strong solid fluorescence with a longer wavelength emission and larger Stokes shift. In addition, NIM-3 showed unexpected blue-green fluorescence due to the formation of fluorescent organic nanoparticles (FONs) under mixed solution. These two cases were ascribed to the aggregation-induced enhanced emission (AIEE) effects and which can also reasonably explain the bright cellular images observed when cells were incubated with NIM-2 and NIM-3. Furthermore, compound NIM-2 can be used to recognize cancer cells owing to its subcellular behaviour

Predictors for Early and Late Death in Adult Patients with COVID-19: A Cohort Study

The timing of death in patients with coronavirus disease 2019 (COVID-19) varied by their comorbidities and severity of illness. However, few studies have determined predictors of mortality with respect to the timing of death in infectious patients. This cohort study aimed to identify the factors associated with early and late death in hospitalized COVID-19 patients. From 14 May to 31 July 2021, this study consecutively recruited laboratory-confirmed COVID-19 patients admitted to Taipei City Hospital. All patients with COVID-19 were followed up until death or discharge from the hospital or till 13 August 2021. Mortality in such patients was categorized as early death (death within the first two weeks of hospitalization) or late death (mortality later than two weeks after hospitalization), based on the timing of death. Multinomial logistic regression was used to determine the factors associated with early and late death among such patients. Of 831 recruited patients, the overall mean age was 59.3 years, and 12.2% died during hospitalization. Of the 101 deceased, 66 (65.3%) and 35 (34.7%) died early and late, respectively. After adjusting for demographics and comorbidities, independent predictors for early death included age &ge; 65 years (adjusted odds ratio (AOR) = 5.27; 95% confidence interval (CI): 2.88&ndash;9.65), heart failure (AOR = 10.32; 95% CI: 2.28&ndash;46.65), and end-stage renal disease (AOR = 11.97; 95% CI: 3.53&ndash;40.55). This study found that two thirds of COVID-19 deaths occurred within two weeks of hospitalization. It suggests that hospitalized patients with COVID-19 should be treated carefully and monitored closely for the progression of clinical conditions during treatment, particularly in older patients and in those with comorbidities