gebhart/patrepeval huggingface dataset:
Productive human herpesvirus 6 infection causes aberrant accumulation of p53 and prevents apoptosis (2004)

p53 plays an important role in tumour suppression in cells exposed to some genotoxic stresses. We found that the p53 protein level was increased in a variety of cell lines infected with human herpesvirus 6 (HHV-6). Because the elevation in p53 began very soon after infection (4 h) and did not occur with UV-inactivated virus infection, it appeared to require the expression of one or more viral immediate-early (IE) genes. To elucidate the mechanism of p53 induction, we investigated its regulation at the protein level. Pulse-chase analysis showed that the stability of p53 increased in HHV-6-infected cells. In addition, the ubiquitination of p53 decreased after infection, indicating that the stability of p53 was increased through deubiquitination. We showed by confocal microscopy that the additional p53 mainly localized to the cytoplasm and that p53 was retained in the cytoplasm even after UV irradiation, but that it translocated into the nucleus in mock-infected cells. Furthermore, DNA fragmentation analysis, a terminal deoxynucleotidyl transferase-mediated dUTP nick end-labelling (TUNEL) assay and annexin V staining showed that infected cells were resistant to UV-induced apoptosis. These results lead us to propose that HHV-6 has a mechanism for retaining p53 within the cytoplasm and protects the infected cells from apoptosis.
Molecular Surveillance of True Nontypeable Haemophilus influenzae: An Evaluation of PCR Screening Assays (2012)

Our data suggest an evolutionary continuum between NTHi and Hh and therefore no single gene target could completely differentiate NTHi from Hh. The hpd#3 real time PCR assay proved to be the superior method for discrimination of NTHi from closely related Haemophilus species with the added potential for quantification of H. influenzae directly from specimens. We suggest the hpd#3 assay would be suitable for routine NTHi surveillance and to assess the impact of antibiotics and vaccines, on H. influenzae carriage rates, carriage density, and disease.
Structure and Chemical Behavior of an η5-(1-Azapentadienyl)lithium Derivative Generated by Deprotonation Reactions Starting from 9-(N-tert-Butylaminomethyl)fluorene or 6-(tert-Butylamino)dibenzofulvene (1997)

Fluorenyllithium (1) adds to tert-butyl isocyanate to yield 9-(N-tert-butylcarboxamido)fluorenyllithium (3). Its reduction with LiAlH4 followed by aqueous workup leads to the formation of the corresponding dibenzo-N-tert-butylaminofulvene 5. Treatment of 5 with sodium cyanoborohydride furnishes 9-(N-tert-butylaminomethyl)fluorene (6). Deprotonation of the fulvene 5 with n-butyllithium in ether yields the η5-azapentadienyllithium derivative 11. The X-ray crystal structure analysis of 11·(Et2O)2 reveals a nearly planar U-shaped 1-azapentadienyl moiety that exhibits five close contacts to the lithium atom located above the ligand plane. Computational chemistry (PM3) has identified the η5-(1-azapentadienyl)lithium derivative 11 as a global minimum. In solution compound 11 undergoes a dynamic degenerate rearrangement process that is rapid on the 1H NMR time scale. It equilibrates the annulated arene moieties of 11. The Gibbs activation energy of this symmetrization process is ΔG⧧enant = 11.8 ± 0.3 kcal mol-1. A Cs-symmetric transition state geometry (11-TS) where the 1-azapentadienyl conjugation is interrupted between C9−C10 was identified by the PM3 calculation. Deprotonation of 9-(N-tert-butylaminomethyl)fluorene (6) gives rise to several competing pathways. Treatment with lithium hexamethyldisilazide leads to abstraction of the fluorenyl 9-H proton to produce the aminomethyl-substituted fluorenyl anion 7. Subsequent treatment of 7 with tert-butyllithium gives the dilithio compound 10. The reaction of 6 with n-butyllithium leads to the formation of a mixture of fluorenyllithium (1) and the η5-(1-azapentadienyl)lithium derivative 11. Deprotonation of 6 with tert-butyllithium furnishes 1 and the dilithiated compound 10. Single crystals of 1·Et2O were analyzed by X-ray diffraction. The compound shows a polymeric “super-sandwich” structure with an alternating fluorenyl-Li·OEt2 arrangement exhibiting inversion symmetry. The X-ray crystal structure analysis of 10·(THF)3 reveals an unsymmetrical arrangement of the lithium atoms at the amidomethylfluorenyl-“dianion” framework with one THF molecule bridging between the metal centers. The bonding features of the dilithiated system 10 derived by double deprotonation of 6 were also analyzed by computational chemistry.
Academic Centers Are Associated with Improved Survival Outcomes in High Risk Diffuse Large B-Cell Lymphoma Patients (2018)

Abstract Background: Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma, and is characterized as a heterogenous disease associated with varying outcomes. The International Prognostic Index (IPI) has been the standard for baseline prognostic assessment in these patients. In this study we aimed to determine the impact of treatment facility (academic versus non-academic centers) on overall survival outcomes in DLBCL patients stratified by IPI score risk groups, with a focus on high risk disease as this is associated with poorer outcomes. Methods: The 2018 National Cancer Database (NCDB) was utilized for patients diagnosed with DLBCL between 2004-2015. Patients were then stratified based on IPI risk score from low to high risk. Four risk groups were formed: low (0-1), low-intermediate (2), high-intermediate (3), and high (4-5). Overall survival was calculated using Kaplan-Meyer analysis with bivariate cox proportional hazard ratios to compare survival by facility type (academic or community centers) within these risk groups. Results: A total of 160,137 patients were identified. Of these cases 31.8% were classified as low risk, 21.9% were low-intermediate risk, 22.2% were high-intermediate risk, and 24% were high risk. 59.3% of patients were treated at a community center and 40.7% were treated at academic centers. Treatment at academic centers was associated with a significantly improved overall survival (OS) for each risk category. Median survival (in months) for high risk IPI score DLBCL was 47.9 months in community and 61.1 months in academic centers (p&lt;.0001). Median survival for high-intermediate risk score was 48.3 months in community and 87.3 months in academic centers (p&lt;.0001). Median survival for low-intermediate score was 90.3 months in community and 122.8 months in academic centers (p&lt;.0001). Median survival for low risk score was 132 months in community and 148 months in academic centers (p&lt;.0001). Hazard ratios for academic center versus community center for high risk, high-intermediate, low-intermediate and low risk are 0.768, 0.71, 0.848 and 0.818 respectively (p&lt;.0001). Conclusions: Facility type is significantly associated with improved survival outcomes across all IPI based risk groups for DLBCL. This benefit is especially significant in higher risk disease where positive outcomes are less common, suggesting treatment at academic centers may be particularly beneficial in these patients. Some of the possible reasons for this difference may include provider experience, increased access to resources, and opportunity for clinical trials. Further investigations into the factors contributing to such disparities should be done to help standardize care and improve outcomes. Disclosures No relevant conflicts of interest to declare.
Quantitative, Label-Free Detection of the Aggregation ofα-Synuclein Using Microcantilever Arrays Operated in a Liquid Environment (2011)

Early detection of protein aggregation is of great importance in the field of neurodegenerative diseases. The successful detection of the aggregation of the protein α -synuclein in a quantitative, label-free manner by functionalising a microcantilever with α -synuclein monomers and operating it in dynamic mode in the presence of α -synuclein monomers in solution is reported. A total mass of 6 ng of α -synuclein was detected over 9 hours on the surface of the cantilever. The result is compared to conventional fluorescence measurements of α -synuclein aggregation under similar conditions. It is found that the label-free cantilever detection method requires a concentration of protein 50 times smaller than that of the current method and indicated potential for significantly faster response times.
Pre-screening and preventive quarantine likely explains the low SARS-CoV-2 prevalence among Norwegian conscripts (2021)

<b>Objective:</b> We aim to discuss whether preventive quarantine can mitigate the spread of Covid-19 during the pandemic. <b>Design:</b> We did a cross-sectional, observational study design in a mass-screening program in the enrolment to the Norwegian military during April 19-28th 2020 (COVID-NOR-MIL). <b>Subjects:</b> 1170 presumptively healthy young Norwegian conscripts. <b>Setting:</b> A structured interview encouraged the coming conscripts to a self-imposed preventive quarantine the last two weeks before enrolment. <b>Main outcome measures:</b> All conscripts underwent a PCR-based test with nasopharyngeal swabs at the day of enrolment. <b>Results:</b> Only two tested positive. The study discusses the predictive value of the RT-PCR test and the risk of false positive and false negative results, particularly when using the test in a low-prevalent cohort, even if the test properties of sensitivity and specificity is almost 100%. Further, the study discusses the challenge of whether a positive SARS-CoV-2 PCR-test represent viable and contagious virus or only viral remnants. <b>Conclusion:</b> The adherence to self-imposed preventive quarantine is a challenge and is a subject to further research. Implications: We want to draw the attention to the potential value of a thorough pre-screening processes and self-imposed preventive quarantine to minimize the potential spread of SARS-Cov-2.
ISOLATION OF STREPTOMYCIN FROM A PINK VARIANT OF S. GRISEUS (1948)

As one of the most important antibiotics, streptomycin has been studied in detail by many workers after the discovery of Waksman and his colleagues (1), but it has been a very difficult work to isolate a streptomycin-producing strain, until recently the above author (2) found a rapid isolation method. Thereafter several active strains were isolated also by us (3) and afterwards two strains by other Japanese workers in obedience to our publication (3) . The fact that all active strains obtained both in America and in Japan belong to S. griseus seems to suggest the existence of a specific relation betweenn streptomycin and S. griseus. But hitherto an antibiotic substance has been usually obtained from more than. one species, such as penicillin from P. chrysogenum notatum, A. flavus and etc, Patulin from P. patulum, P. expansum, P. leucopus, P. claviforme and A. clavatus, While we were classifing numerous antibiotic strains of strepomyces according to their antibacterial spectra, we found several strains producing a pink pigment and possessing the streptomycin-producing ability. Waksman and others (4) recently observed Streptomyces bikiniensis to produce a streptømycin-like substance, however these strains seem to be different from this strain. The antibiotic obtained from our strains conforms to streptomycin in its antibácterial spectrum, toxicity, solubility in various solvents and colour of Sakaguchi's reaction.Present paper describes the isolation of the strains, and various foundations to decide it to be streptomycin. The characters of the strain in detail will be published elsewhere.
Effect of milk peptides that enhance iron uptake by Caco‐2 cells on the expression of DMT‐1 and on iron dialyzability from meals (2008)

Biologically active peptides may be formed during milk digestion. We have shown that in vitro digestion of milk produces peptides that enhance iron uptake by Caco‐2 cells. Our objectives were to investigate whether these peptides a) may exert their effect by increasing relative gene expression of DMT1 in Caco‐2 cells b) may enhance iron dialyzability when added in meals. An in vitro digest of cow's milk was fractionated by gel filtration. Selected fractions were incubated with Caco‐2 cells for 2 or 48 hours. Relative gene expression of DMT1 was not different between peptide treatments and the control. Isolated milk peptides were mixed with iron in milk or in a vegetable or in a fruit meal and subjected to an in vitro digestion, modified to allow the processing of small volumes. Peptides enhanced iron dialyzability from water by more than two fold, but did not have any effect on iron dialyzability from milk or from meals. However, lyophilized peptides produced an enhancing effect on iron dialyzability from milk. Our results suggest that selected isolated milk peptides may not affect expression of DMT‐1. Milk peptides preserve their enhancing properties after in vitro digestion but they have a limited effect on iron dialyzability from meals depending on their concentration. This research project is co‐financed by E.U.‐European Social Fund (75%) and the Greek Ministry of Development‐GSRT (25%).
A Synthetic DNA‐Binding Domain Guides Distinct Chromatin‐Modifying Small Molecules to Activate an Identical Gene Network (2015)

Abstract Synthetic dual‐function ligands targeting specific DNA sequences and histone‐modifying enzymes were applied to achieve regulatory control over multi‐gene networks in living cells. Unlike the broad array of targeting small molecules for histone deacetylases (HDACs), few modulators are known for histone acetyltransferases (HATs), which play a central role in transcriptional control. As a novel chemical approach to induce selective HAT‐regulated genes, we conjugated a DNA‐binding domain (DBD) “I” to N ‐(4‐ c hloro‐3‐trifluoromethyl‐phenyl)‐2‐ethoxy‐benzamide (CTB), an artificial HAT activator. In vitro enzyme activity assays and microarray studies were used to demonstrate that distinct functional small molecules could be transformed to have identical bioactivity when conjugated with a targeting DBD. This proof‐of‐concept synthetic strategy validates the switchable functions of HDACs and HATs in gene regulation and provides a molecular basis for developing versatile bioactive ligands.
Evaluating the Benefits of Zipper Fracs in Unconventional Reservoirs (2014)

Abstract In cemented and cased wells, perforation cluster spacing is optimized based on the type of reservoir fluid, permeability, fracture conductivity, proppant distribution, and associated stresses to place multiple fractures along horizontal wellbores. Specifically, in very low-permeability reservoirs, the requirement for smaller perforation or fracture spacing might not be possible because of the geomechanical interference between fractures. In this case, the commonly used zipper-frac technique can provide a means to create fractures in projects with closer spacing. The benefits of zipper fracs can be maximized by generating proper fracture geometry and properly staggering the perforation/fracture system. This paper reviews and discusses numerical reservoir-modeling results of zipper fracturing that demonstrate the individual or combined effects of the perforation/fracture staggering, comparing these to the fracture length, fracture overlap, fracture conductivity, and/or proppant distribution effects of a conventional completion that does not use the staggered zipper-frac approach. The simulation results are assessed over a wide range of unconventional reservoir permeabilities for both gas and light oil.
Luminance-Based Multi-Scale Retinex (1997)

Multi-scale retinex (MSR) processing has been shown to be an effective way to enhance image contrast, but it often has an undesirable desaturating effect on the image colours. A colourrestoration method [2,3] can help mitigate this effect, but our experience is that it simply leads to other problems. In this paper we modify MSR so that it preserves colour fidelity while still enhancing contrast. We then add neural-net based colour constancy processing [7] to this modified version of MSR. The result is a principled approach that provides the contrast-enhancement benefits of MSR and improved colour fidelity.
Periodic Surface Energy Driven Single Crystallization on Flat Surface (1985)

This letter demonstrates the single crystallization of thin films on unordered substrates (amorphous materials) with a discrete surface energy distribution, even if the substrate surface is flat. This crystallization, called periodic surface energy driven single crystallization, arises from the periodic stripe patterns of different materials with different surface energy. An example that facetted KCl single crystals can be grown on the SiO 2 -Si 3 N 4 stripe patterns is shown.
Changing the attitude towards magnetoresistance (2011)

Magnetometers are one of the most common instruments on spacecrafts. They are used for both satellite attitude determination and for scientific purposes, such as mapping of Earth’s magnetic field. The most common magnetometer for low-frequency applications is the fluxgate. High-end fluxgates are generally quite bulky, with a mass of around 1 kg, but there exist miniature version, weighing only around 100 g, but with worse noise figure. Interest in such miniature models has increased with the adaption of the Faster-Better-Cheaper philosophy, and the introduction of small satellite classes. However, downscaling of fluxgates beyond the present 100 g has proven difficult, wherefore other technologies have earned more and more interest, especially those employing different kinds of magnetoresistance.Here, a review of different magnetoresistive techniques, and their past, present and potential use in space is presented. Magnetoresistive sensors based on anisotropic, giant, and tunneling magnetoresistance is covered, and extra attention is directed towards sensors based on the planar Hall effect. The latter have the potential of overcoming some of the major disadvantages of other magnetoresistive sensors, such as poor detectivity at low frequencies, and the need for external biasing coils to improve linearity and reduce hysteresis by, e.g., set-reset protocols and magnetic feedback.Moreover, the design of two such planar Hall effect sensors is tailored to meet the requirements set on a magnetometer aimed for, firstly, attitude determination and, secondly, mapping of Earth’s magnetic field. It is concluded that planar Hall effect sensors is one of the prime candidates for the next generation of miniaturized low-frequency space magnetometers.
IL-1 Receptor-Mediated Signal Is an Essential Component of MyD88-Dependent Innate Response to Mycobacterium tuberculosis Infection (2007)

MyD88, the common adapter involved in TLR, IL-1, and IL-18 receptor signaling, is essential for the control of acute Mycobacterium tuberculosis (MTB) infection. Although TLR2, TLR4, and TLR9 have been implicated in the response to mycobacteria, gene disruption for these TLRs impairs only the long-term control of MTB infection. Here, we addressed the respective role of IL-1 and IL-18 receptor pathways in the MyD88-dependent control of acute MTB infection. Mice deficient for IL-1R1, IL-18R, or Toll-IL-1R domain-containing adaptor protein (TIRAP) were compared with MyD88-deficient mice in an acute model of aerogenic MTB infection. Although primary MyD88-deficient macrophages and dendritic cells were defective in cytokine production in response to mycobacterial stimulation, IL-1R1-deficient macrophages exhibited only a reduced IL-12p40 secretion with unaffected TNF, IL-6, and NO production and up-regulation of costimulatory molecules CD40 and CD86. Aerogenic MTB infection of IL-1R1-deficient mice was lethal within 4 wk with 2-log higher bacterial load in the lung and necrotic pneumonia but efficient pulmonary CD4 and CD8 T cell responses, as seen in MyD88-deficient mice. Mice deficient for IL-18R or TIRAP controlled acute MTB infection. These data demonstrate that absence of IL-1R signal leads to a dramatic defect of early control of MTB infection similar to that seen in the absence of MyD88, whereas IL-18R and TIRAP are dispensable, and that IL-1, together with IL-1-induced innate response, might account for most of MyD88-dependent host response to control acute MTB infection.
Transform coefficient coding design for AVS2 video coding standard (2013)

AVS2 is a next-generation audio and video coding standard currently under development by the Audio Video Coding Standard Workgroup of China. In this paper, a coefficient-group based transform coefficient coding design for AVS2 video coding standard is presented, which includes two main coding tools, namely, two-level coefficient coding and intra-mode based context design. The two-level coefficient coding scheme allows accurate coefficient position information to be used in the context model design and improves the coding efficiency. It also helps increase the entropy coding throughput and facilitate parallel implementation. The intra-mode based context design further improves coding performance by utilizing the intra-prediction mode information in the context model. The two coding tools combined provide consistent rate-distortion performance gains under standard test conditions. Both tools were adopted into the AVS2 working draft. Furthermore, an improved rate-distortion optimized quantization algorithm is designed based on the proposed scheme, which significantly reduces the encoder complexity.
Contour interaction under photopic and scotopic conditions (2018)

In the present study, we asked whether contour interaction undergoes significant changes for different luminance levels in the central and peripheral visual field. This study included nine normal observers at two laboratories (five at Palacky University Olomouc, Czech Republic and four at the University of Houston, USA). Observers viewed a randomly selected Sloan letter surrounded by four equally spaced bars for several separations measured edge-to-edge in min arc. Stimuli were viewed foveally under photopic and mesopic luminances and between 5° and 12° peripherally for four different background luminances of the display monitors, corresponding to photopic, mesopic, scotopic, and dim scotopic levels. The extent of the contour interaction in the fovea is approximately 20 times smaller than in the periphery. Whereas the magnitude of foveal contour interaction markedly decreases with decreasing luminance, no consistent luminance-induced change occurs in peripheral contour interaction. The extent of contour interaction does not scale with the size of the target letter, either in the fovea or peripherally. The results support a neural origin of contour interaction consistent with the properties of center-surround antagonism.
Gradient-based Hierarchical Clustering using Continuous Representations of Trees in Hyperbolic Space (2019)

Hierarchical clustering is typically performed using algorithmic-based optimization searching over the discrete space of trees. While these optimization methods are often effective, their discreteness restricts them from many of the benefits of their continuous counterparts, such as scalable stochastic optimization and the joint optimization of multiple objectives or components of a model (e.g. end-to-end training). In this paper, we present an approach for hierarchical clustering that searches over continuous representations of trees in hyperbolic space by running gradient descent. We compactly represent uncertainty over tree structures with vectors in the Poincare ball. We show how the vectors can be optimized using an objective related to recently proposed cost functions for hierarchical clustering (Dasgupta, 2016; Wang and Wang, 2018). Using our method with a mini-batch stochastic gradient descent inference procedure, we are able to outperform prior work on clustering millions of ImageNet images by 15 points of dendrogram purity. Further, our continuous tree representation can be jointly optimized in multi-task learning applications offering a 9 point improvement over baseline methods.