Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying reference to abstract objects in dialogue

In two experiments, many annotators marked antecedents for discourse deixis as unconstrained regions of text. The experiments show that annotators do converge on the identity of these text regions, though much of what they do can be captured by a simple model. Demonstrative pronouns are more likely than definite descriptions to be marked with discourse antecedents. We suggest that our methodology is suitable for the systematic study of discourse deixis.
A new method for the estimation of time difference of arrival for localization of partial discharge sources using acoustic detection technique

In an acoustic partial discharge (PD) detection system, estimation of time difference of arrival (TDOA) between acoustic signals arriving at a sensor array is an important criterion for accurate localization of PD sources inside a transformer. The localization accuracy can be improved by improving the accuracy of estimation of TDOA between sensors. The estimation of TDOA is a challenging task because acoustic signals are corrupted by noise, reverberation, echo and reflection of acoustic signals inside the transformer tank. Keeping this in mind, this paper presents a technique for the accurate estimation of TDOA by extraction of an estimate of the PD pulse from the recorded acoustic signals. The TDOA between two sensors is then calculated by finding the cross-correlation function between the two sensors. The acoustic path through the transformer tank and oil constitutes the physical system, which when excited by the PD pulse, gives rise to the acoustic pressure waves. An estimate of the PD pulse, which generates the acoustic pressure waves, may therefore be obtained by separating the acoustic response of the tank-oil physical system from the acoustic signal. The extracted PD pulse information gives an estimate of the instant of appearance of the PD pulse at each sensor, which makes the accurate estimation of TDOA possible.
Involvement of Efflux Pumps in the Resistance to Peptidoglycan Synthesis Inhibitors in Mycobacterium tuberculosis

ABSTRACT We evaluated the contributions of Mycobacterium tuberculosis efflux pumps towards intrinsic resistance to different classes of peptidoglycan synthesis inhibitors (PSI). Our study indicates that the efflux pump knockout strains are more susceptible to PSI than the wild type. Vancomycin and ceftriaxone exhibited up to 3 log increased kill on efflux pump mutants compared to the wild-type strain, strongly suggesting an important role for efflux pumps in the intrinsic resistance of M. tuberculosis to PSI.
Prognostic Radiology: Quantitative Assessment of Tumor Oxygen Dynamics by MRI

It is generally recognized that tumor hypoxia has a strong influence over therapeutic outcome in the clinic. The authors have developed an oximetry approach using 19F echo planar magnetic resonance imaging–FREDOM (Fluorocarbon Relaxometry using Echoplanar imaging for Dynamic Oxygen Mapping), which reveals dynamic changes based on sequential maps of regional tumor Po2. Preclinical investigations focused on diverse sublines of the Dunning prostate R3327 tumor. As expected, intratumoral heterogeneity was considerable. However, large tumors (>3.5 cm3) were significantly less well oxygenated than smaller tumors (<2 cm3). Faster growing, less differentiated tumors were less well oxygenated than size-matched tumors of slower growing sublines. The greatest potential of this technique is the ability to follow the fate of individual tumor regions with respect to interventions. For each subline, there was a significant response to respiratory challenge with oxygen for initially well-oxygenated regions (baseline Po2 > 10 mm Hg). More interestingly, subline dependent behavior was found for initially hypoxic regions that correlated with rate of growth. The authors believe the FREDOM approach is essentially ripe for translation to the clinic. This approach could help to identify patients with hypoxic tumors and indicate the feasibility of manipulating tumor characteristics through adjuvant interventions to improve therapeutic response.
Identification of 23-(S)-2-Amino-3-Phenylpropanoyl-Silybin as an Antiviral Agent for Influenza A Virus Infection In Vitro and In Vivo

ABSTRACT It has been reported that autophagy is involved in the replication of many viruses. In this study, we screened 89 medicinal plants, using an assay based on the inhibition of the formation of the Atg12-Atg5/Atg16 heterotrimer, an important regulator of autophagy, and selected Silybum marianum L. for further study. An antiviral assay indicated that silybin (S0), the major active compound of S. marianum L. , can inhibit influenza A virus (IAV) infection. We later synthesized 5 silybin derivatives (S1 through S5) and found that 23-(S)-2-amino-3-phenylpropanoyl-silybin (S3) had the best activity. When we compared the polarities of the substituent groups, we found that the hydrophobicity of the substituent groups was positively correlated with their activities. We further studied the mechanisms of action of these compounds and determined that S0 and S3 also inhibited both the formation of the Atg12-Atg5/Atg16 heterotrimer and the elevated autophagy induced by IAV infection. In addition, we found that S0 and S3 could inhibit several components induced by IAV infection, including oxidative stress, the activation of extracellular signal-regulated kinase (ERK)/p38 mitogen-activated protein kinase (MAPK) and IκB kinase (IKK) pathways, and the expression of autophagic genes, especially Atg7 and Atg3. All of these components have been reported to be related to the formation of the Atg12-Atg5/Atg16 heterotrimer, which might validate our screening strategy. Finally, we demonstrated that S3 can significantly reduce influenza virus replication and the associated mortality in infected mice. In conclusion, we identified 23-(S)-2-amino-3-phenylpropanoyl-silybin as a promising inhibitor of IAV infection.
V-79 Chinese Hamster cells irradiated with antiprotons, a study of peripheral damage due to medium and long range components of the annihilation radiation

Purpose: Radiotherapy of cancer carries a perceived risk of inducing secondary cancer and other damage due to dose delivered to normal tissue. While expectedly small, this risk must be carefully analysed for all modalities. Especially in the use of exotic particles like pions and antiprotons, which annihilate and produce a mixed radiation field when interacting with normal matter nuclei, the biological effective dose far out of field needs to be considered in evaluating this approach. We describe first biological measurements to address the concern that medium and long range annihilation products may produce a significant background dose and reverse any benefits of higher biological dose in the target area. Materials and methods: Using the Antiproton Decelerator (AD) at CERN (Conseil Européen pour la Recherche Nucléaire) we irradiated V-79 Chinese Hamster cells embedded in gelatine using an antiproton beam with fluence ranging from 4.5 × 108 to 4.5 × 109 particles, and evaluated the biological effect on cells located distal to the Bragg peak using clonogenic survival and the COMET assay. Results: Both methods show a substantial biological effect on the cells in the entrance channel and the Bragg Peak area, but any damage is reduced to levels well below the effect in the entrance channel 15 mm distal to the Bragg peak for even the highest particle fluence used. Conclusions: The annihilation radiation generated by antiprotons stopping in biological targets causes an increase of the penumbra of the beam but the effect rapidly decreases with distance from the target volume. No major increase in the biological effect is found in the far field outside of the primary beam.
[Study on HPLC fingerprint characteristic analysis of Cordyceps sinensis and its similar products].

OBJECTIVE To study on HPLC fingerprint characteristic analysis of Cordyceps sinensis and its similar products. METHODS To determinate 13 samples of Cordyceps sinensis and its similar products by HPLC, and analyze the HPLC results with similar appraisal method and graphical methods of multivariate sample in two dimensional plane such as the methods of profile, radar chart and constellation graph. RESULTS The similar appraisal method might synthesize the similar degree in quantification, while the graphical methods such as profile graph, radar chart and constellation graph could show more details about the classification and the characteristic of varieties directly. CONCLUSIONS We recommend the combined application of similar appraisal method and the graphical methods due to its advantages on the judgment and characteristic analysis of fingerprint.
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring.

In shotgun proteomics, tandem mass spectra of peptides are typically identified through database search algorithms such as Sequest. We have developed DirecTag, an open-source algorithm to infer partial sequence tags directly from observed fragment ions. This algorithm is unique in its implementation of three separate scoring systems to evaluate each tag on the basis of peak intensity, m/ z fidelity, and complementarity. In data sets from several types of mass spectrometers, DirecTag reproducibly exceeded the accuracy and speed of InsPecT and GutenTag, two previously published algorithms for this purpose. The source code and binaries for DirecTag are available from http://fenchurch.mc. vanderbilt.edu.
Engineering porous polyurethane scaffolds by photografting polymerization of methacrylic acid for improved endothelial cell compatibility.

Using a preadsorbing-monomer method, polyurethane (PU) porous scaffolds were modified by grafting polymerization of methacrylic acid (MAA) initiated under UV light. Fourier transform infrared-attenuated total reflection spectroscopy and X-ray photoelectron spectroscopy characterizations confirmed the occurrence of the grafting polymerization of poly(methacrylic acid) (PMAA) on PU scaffolds and the measurement of water adsorption also demonstrated enhanced hydrophilicity. The PMAA grafting degree correlated to the amount of MAA adsorbed, the pore average diameter, and the porosity. It was verified that the higher porosity the scaffold has, the larger porous area (or the larger contact area with MAA) it has, and therefore the higher amount of MAA adsorbed and higher grafting degree obtained. The results of human endothelial cells cultured in vitro showed that the PU scaffolds modified with the hydrophilic PMAA had more improved cell compatibility than the control matrix.
Donor Desmopressin Is Associated With Superior Graft Survival After Kidney Transplantation

Background. A recent randomized trial showed that pretreatment of the brain-dead donor with low-dose dopamine improves immediate kidney graft function, by limiting injury from cold storage (ClinicalTrials.gov Identifier: NCT00115115). This study determines whether donor exposure to desmopressin (1-deamino-8-d-arginine-vasopressin [DDAVP]) before organ retrieval affects renal transplant outcome. Methods. This retrospective multicenter cohort study, nested in the database of the dopamine trial, includes 264 deceased heart-beating donors with confirmed brain death and corresponding 487 renal allograft recipients transplanted at 60 European centers between March 2004 and August 2007. We assessed differences in delayed graft function, biopsy-proven acute rejections, and 2-year kidney graft survival in recipients of a DDAVP-exposed versus unexposed graft. Results. DDAVP was associated with improved graft survival (85.4% vs. 73.6%, P=0.003). This survival benefit persisted after censoring for death with functioning graft (91.1% vs. 82.0%, P=0.01) and after adjustment for confounders including covariate adjustment from propensity scoring (hazard ratio 0.40, 95% confidence interval [CI] 0.21–0.77; P=0.006). Delayed graft function (odds ratio 0.97, 95% CI 0.57–1.65; P=0.92) and biopsy-proven acute rejections (odds ratio 1.32, 95% CI 0.70–2.49; P=0.40) were unaffected. The survival effect was enhanced after a shorter cold ischemic time less than 14 hr (91.3% vs. 77.8%, P=0.008) and after dopamine pretreatment (92.7% vs. 78.6%, P=0.006). By contrast, prolonged cold ischemic time more than or equal to 14 hr (91.2% vs. 86.5%, P=0.39) and assignment to the nondopamine group (89.7% vs. 84.8%, P=0.37) abrogated the survival advantage. Conclusions. Donor DDAVP seems to improve renal allograft survival. Combined use of donor DDAVP and low-dose dopamine should receive further evaluation.
Epidemiology: Culture of bovine bone marrow progenitor cells in vitro

Summary In vitro methylcellulose cultures of bovine bone marrow progenitor cells were developed. An existing technique described for bovine species was compared to a method for human tissue and further adapted during subsequent experiments. Bovine bone marrow samples were collected at the slaughterhouse, and mononuclear cells were separated by gradient centrifugation (1.077 g/ml specific density and 400g). The use of 3% bovine leucocyte‐conditioned medium, produced by stimulation of blood lymphocytes with 4 pg/ml concanavalin A and harvested on day 4 of culture, gave better results than the use of supernatant of the human bladder carcinoma 5637, which is widely used in human bone marrow cultures. However, bovine leucocyte‐conditioned medium was not added to erythroid cultures because inhibitory effects were observed. Erythroid colonies were stimulated with erythropoietin, and hemin was added to enable microscopic identification. Reduced oxygen tension was necessary to induce growth of erythroid colonies. This was not necessary for myeloid cultures. In conclusion, the results of this study show that the growth of myeloid and erythroid colonies in methylcellulose‐based medium requires different culture conditions, which are different from the culture conditions for human cells.
Visualization of Leaf Botanical Features Extracted from AlexNet Convolutional Layers

To recognize tree species from pictures of their leaves, one way is to automatically extract the features botanists look at for identification and use them in a classification system. This is the approach developed in the Folia application. Another way that has emerged in the past years is to train Convolutional Neural Networks (CNN) to recognize plants directly from pictures, as done by many researchers in the PlantCLEF challenge. CNN-based methods have spread into many fields as they generally give the best results, but can arguably be considered a black box. The aim of our work is to try to understand their core and establish a link between the features extracted through such networks and botanical characteristics of the species, in order to improve expressiveness and propose alternative recognition algorithms. For our study, we worked with the widely used AlexNet network. Its performances are inferior to those of the most recent CNN (GoogLeNet, ResNet, VGGNet) but its linear architecture allows to visualize more easily the different convolutional layers. Thus, we chose to train AlexNet on an image database of 72 simple-leaved species developed by the PlantCLEF challenge, where leaves are shot on a plain color sheet (no complex background). We trained AlexNet from scratch to construct its convolutional filters directly on plant organ elements. As the entry of AlexNet is a 256x256 image, the images have been resized and filled with random values on the borders to preserve the aspect ratio of the leaves. Then, we have visualized the obtained filters and analysed them.
A rare case of breakthrough fungal pericarditis due to fluconazole‐resistant Candida auris in a patient with chronic liver disease

Introduction: Candida pericarditis is a rare clinical entity with a high fatality, primarily attributed to difficulty in diagnosis. Unfortunately, the diagnosis is made post‐mortem in more than 50% of cases, and thus a high index of clinical suspicion is crucial. Case presentation: We report a rare case of fungal pericardial effusion caused by the recently recognized multidrug‐resistant Candida auris, which was cultured from pericardial fluid, blood, bronchoalveolar lavage and urine of a chronic liver disease patient while on empiric fluconazole therapy. The yeast was misidentified as Candida haemulonii by the VITEK2 commercial identification system, and was confirmed as C. auris by internal transcribed spacer and large ribosomal subunit sequencing. In addition, the VITEK2 AST card erroneously revealed a high amphotericin B MIC (16 µg ml−1) and low caspofungin MIC (0.25 µg ml−1) that did not correlate with results from the reference Clinical and Laboratory Standards Institute (CLSI) microbroth dilution method. Based on VITEK2 MIC data, the patient was administered caspofungin. However, in vitro antifungal susceptibility data for C. auris by the CLSI method exhibited high MICs to fluconazole (64 µg ml−1) and caspofungin MIC (1 µg ml−1) but low MICs to amphotericin B (MIC range, 0.125−0.5 µg ml−1). The patient’s repeat pericardial fluid culture, despite caspofungin therapy for 12 days, grew C. auris and he died on day 13 of therapy. Conclusion: C. auris is a recently reported agent of fungaemia and deep‐seated infections and is notable for its antifungal resistance. Although early species identification and rapid antifungal susceptibility testing are needed in cases of critical infections, the reporting of rare yeast isolates exhibiting high MICs to antifungals by automated systems needs a cautionary approach.
Unilateral intraputamenal glial cell line-derived neurotrophic factor in patients with Parkinson disease: response to 1 year of treatment and 1 year of withdrawal.

OBJECT Glial cell line-derived neurotrophic factor (GDNF) infused unilaterally into the putamen for 6 months has been previously shown to improve significantly motor functions and quality of life measures in 10 patients with Parkinson disease (PD) in a Phase I trial. In the present study the authors report the safety and efficacy of continuous treatment for a minimum of 1 year. After the trial was halted by the drug sponsor, the patients were monitored for an additional 1 year during which the effects of drug withdrawal were evaluated. METHODS During the extended study period, patients received a 30-microg/day unilateral intraputamenal infusion of GDNF at a basal infusion rate supplemented with pulsed boluses every 6 hours at a convection-enhanced delivery rate to increase tissue penetration of the protein. When the study was stopped, the delivery system was reprogrammed to deliver sterile saline at the basal infusion rate of 2 microl/hour. The Unified Parkinson's Disease Rating Scale (UPDRS) total scores after 1 year of therapy were improved by 42 and 38% in the off- and on-medication states; the motor UPDRS scores were also improved 45 and 39%, respectively. Benefits from treatment were lost by 9 to 12 months after the cessation of GDNF infusion. The UPDRS scores returned to their baseline and the patients required higher levels of conventional antiparkinsonian drugs to treat symptoms. After 11 months of treatment, the delivery system had to be removed in one patient because of risk of infection. Seven patients developed antibodies to GDNF but without evident clinical sequelae. There was no evidence for GDNF-induced cerebellar toxicity, as evaluated by magnetic resonance imaging and clinical testing. CONCLUSIONS The unilateral administration of GDNF results in significant, sustained bilateral benefits in patients with PD. These improvements are lost within 9 months of drug withdrawal. Safety concerns with GDNF therapy can be closely monitored and managed.
Targeting of human DNA polymerase ι to the replication machinery via interaction with PCNA

Human DNA polymerase ι (hPolι) promotes translesion synthesis by inserting nucleotides opposite highly distorting or noninstructional DNA lesions. Here, we provide evidence for the physical interaction of hPolι with proliferating cell nuclear antigen (PCNA), and show that PCNA, together with replication factor C (RFC) and replication protein A (RPA), stimulates the DNA synthetic activity of hPolι. In the presence of these protein factors, on undamaged DNA, the efficiency (Vmax/Km) of correct nucleotide incorporation by hPolι is increased ≈80–150-fold, and this increase in efficiency results from a reduction in the apparent Km for the nucleotide. PCNA, RFC, and RPA also stimulate nucleotide incorporation opposite the 3′-T of the (6) thymine–thymine (T-T) photoproduct and opposite an abasic site. The interaction of hPolι with PCNA implies that the targeting of this polymerase to the replication machinery stalled at a lesion site is achieved via this association.
Natalizumab in multiple sclerosis: proceed with caution?

Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating disease of the CNS. In a Phase II clinical trial, natalizumab was shown to reduce the relapses in patients with relapsing MS, without improving the disability score. After 1-year of Phase III clinical trials, natalizumab was approved by the FDA for use in relapsing MS but was withdrawn 3 months later, due to two reported cases of progressive multifocal leukoencephalopathy (PML). The completed clinical trials with natalizumab for relapsing MS have recently been reported. In a trial of 1171 subjects with relapsing MS, natalizumab alone was shown to reduce the relapse rate and lesions, without causing PML. Although natalizumab was also shown to reduce the relapse rates and lesions in patients taking IFN-β, two cases of PML with natalizumab occurred in these patients. An assessment of patients who had taken natalizumab for 1 – 2 years (∼ 3000), showed the incidence of PML to be 1/1000. A drug that is useful in relapsing MS will be used as a long-term therapy in large numbers of patients. For instance, in the 3 months that natalizumab was registered, 5000 patients commenced taking it. In the author’s opinion, large numbers of patients should not be allowed to take natalizumab until its safety has been monitored in the long-term use in a clinical trial environment.
Countertransference Reactions in Therapeutic Work with Incestuous Sexual Abusers

ABSTRACT The study was a qualitative investigation aimed at therapists' responses to working with a population of incestuous sexual abusers. Semi-structured interviews were conducted with nine therapists who were recruited from psychotherapy, psychology, and forensic psychology services in the National Health Service (NHS) in the UK. The predominant therapeutic model was psychodynamic; however, cognitive-behavioural and integrative approaches were practiced by some therapists. The data were analyzed using interpretative phenomenological analysis (Smith, 1996). Results suggested that the therapists experienced a considerable amount of negative and difficult feelings and that they tended to experience feeling controlled and deceived, which seemed to influence their ability to create and maintain the therapeutic relationship. It was suggested that the dynamics of incestuous sexual abuse played a part in these difficulties. The results are discussed with reference to the clinical therapeutic literature.