gebhart/patrepeval huggingface dataset:
A comprehensive single‐particle model for solid‐state polymerization of poly(L‐lactic acid) (2011)

Abstract We propose here, a comprehensive model for the solid‐state polymerization (SSP) of a low to moderate molecular weight (MW) prepolymer of lactic acid, to produce high MW poly( L ‐lactic acid) (PLLA). The reactions are rationally assumed to occur only in the amorphous region, and effective concentrations of end groups, vary with crystalinity, X c , during SSP. We estimate byproduct diffusivities, D , using free volume theory. The effects of various parameters on the SSP of PLLA prepolymer have been examined with respect to the optimum MW, X c and D . We introduce self‐consistently, scaling factors of ∼ 0.27, in the experimental procedure, to determine via 19 F‐NMR, concentrations of the end groups, after converting them to fluorinated ester groups. The relevant reaction rate constants are obtained by fitting to early time data from representative SSP experiments at 150°C, under high vacuum, on PLLA prepolymer powder (i.e., spherical geometry) of number average MW, M n 0 ∼ 10,200 Da, which attains M n ∼ 150,000 Da, via SSP. The subsequent successful comparison of the model predictions with experimental data throughout the entire SSP duration indicates that the model is comprehensive and accounts for all the relevant phenomena occurring during the SSP to synthesize high MW PLLA. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Differential Regulation of the Melanoma Proteome by eIF4A1 and eIF4E (2016)

Small molecules and antisense oligonucleotides that inhibit the translation initiation factors eIF4A1 and eIF4E have been explored as broad-based therapeutic agents for cancer treatment, based on the frequent upregulation of these two subunits of the eIF4F cap-binding complex in many cancer cells. Here, we provide support for these therapeutic approaches with mechanistic studies of eIF4F-driven tumor progression in a preclinical model of melanoma. Silencing eIF4A1 or eIF4E decreases melanoma proliferation and invasion. There were common effects on the level of cell-cycle proteins that could explain the antiproliferative effects in vitro Using clinical specimens, we correlate the common cell-cycle targets of eIF4A1 and eIF4E with patient survival. Finally, comparative proteomic and transcriptomic analyses reveal extensive mechanistic divergence in response to eIF4A1 or eIF4E silencing. Current models indicate that eIF4A1 and eIF4E function together through the 5'UTR to increase translation of oncogenes. In contrast, our data demonstrate that the common effects of eIF4A1 and eIF4E on translation are mediated by the coding region and 3'UTR. Moreover, their divergent effects occur through the 5'UTR. Overall, our work shows that it will be important to evaluate subunit-specific inhibitors of eIF4F in different disease contexts to fully understand their anticancer actions. Cancer Res; 77(3); 613-22. ©2016 AACR.
Metastasizing tumors from serum-supplemented and serum-free cell lines from a C57BL mouse lung tumor. (1976)

A tissue culture cell line was established from an alveologenic lung carcinoma from a C57BL/lcrf-at mouse. The cells can be maintained in a completely defined serum-free medium. Tumors derived from the tissue culture cells grown in serum-free or serum-supplemented medium give rise to lung metastases. The ultrastructure of the tissue culture cells in both media is similar to that of spontaneous or induced alveologenic mouse lung tumors.
Inflammatory cutaneous reaction to a temporary permanent pacemaker (2021)

The type IV, T cell–mediated hypersensitivity response to intravascular implanted medical devices is well described.1 Though components of pacemaker generators are extravascular, they can contain potentially allergenic compounds and cause clinically relevant adverse allergic reactions that may necessitate device extraction.
Fatigue Behavior of Offshore Topside Structure (2006)

Large-scale model tests of welded topside joints were carried out to observe the fatigue behavior of API 2W Gr.50 steel produced by POSCO. The fatigue crack behaviors for various loading conditions were measured and investigated around the critical joint sections. The experimental results have been verified with numerical approaches and also compared with the AWS D1.1 and DnV RP-C203 design curves. The large-scale experiment models were fabricated, based on the actual operating east area fixed platform. The dimensions of the models were slightly modified to accommodate the test facilities and capacities. The fatigue test was carried out having of T1=705.6kN, T2=749.7kN and T3=793.8kN. The three specimens were statically loaded 20 times, with various loadings of about 50kN intervalsbetween the maximum and minimum loads required in the fatigue tests. This loading removed the residual stress in the specimen before the fatigue tests. The topside joint crack was initiated from the brace heel, where the maximum tensile stress occurred. The API 2W Gr.50 steel satisfied the AWS D1.1 detail category C and DnV RP-C203 detail category F curve.
Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations (2013)

Organism cells proliferate and die to build, maintain, renew and repair it. The cellular history of an organism up to any point in time can be captured by a cell lineage tree in which vertices represent all organism cells, past and present, and directed edges represent progeny relations among them. The root represents the fertilized egg, and the leaves represent extant and dead cells. Somatic mutations accumulated during cell division endow each organism cell with a genomic signature that is unique with a very high probability. Distances between such genomic signatures can be used to reconstruct an organism's cell lineage tree. Cell populations possess unique features that are absent or rare in organism populations (e.g., the presence of stem cells and a small number of generations since the zygote) and do not undergo sexual reproduction, hence the reconstruction of cell lineage trees calls for careful examination and adaptation of the standard tools of population genetics. Our lab developed a method for reconstructing cell lineage trees by examining only mutations in highly variable microsatellite loci (MS, also called short tandem repeats, STR). In this study we use experimental data on somatic mutations in MS of individual cells in human and mice in order to validate and quantify the utility of known lineage tree reconstruction algorithms in this context. We employed extensive measurements of somatic mutations in individual cells which were isolated from healthy and diseased tissues of mice and humans. The validation was done by analyzing the ability to infer known and clear biological scenarios. In general, we found that if the biological scenario is simple, almost all algorithms tested can infer it. Another somewhat surprising conclusion is that the best algorithm among those tested is Neighbor Joining where the distance measure used is normalized absolute distance. We include our full dataset in Tables S1, S2, S3, S4, S5 to enable further analysis of this data by others.
Off-label Use of Tocilizumab in Psoriatic Arthritis: Case Series and Review of the Literature. (2017)

It can be concluded that TCZ cannot be recommended as an alternative treatment for PsA with predominant peripheral involvement.
On-Line Analog Generation of Joint-Interval Histogram (1964)

The joint-interval histogram for adjacent intervals within any temporal sequence of events can be plotted with a simple analog circuit and an oscilloscope.
Exposure of Lycopersicon Esculentum to Microcystin-LR: Effects in the Leaf Proteome and Toxin Translocation from Water to Leaves and Fruits (2014)

Natural toxins such as those produced by freshwater cyanobacteria have been regarded as an emergent environmental threat. However, the impact of these water contaminants in agriculture is not yet fully understood. The aim of this work was to investigate microcystin-LR (MC-LR) toxicity in Lycopersicon esculentum and the toxin accumulation in this horticultural crop. Adult plants (2 month-old) grown in a greenhouse environment were exposed for 2 weeks to either pure MC-LR (100 μg/L) or Microcystis aeruginosa crude extracts containing 100 μg/L MC-LR. Chlorophyll fluorescence was measured, leaf proteome investigated with two-dimensional gel electrophoresis and Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF)/TOF, and toxin bioaccumulation assessed by liquid chromatography-mass spectrometry (LC-MS)/MS. Variations in several protein markers (ATP synthase subunits, Cytochrome b6-f complex iron-sulfur, oxygen-evolving enhancer proteins) highlight the decrease of the capacity of plants to synthesize ATP and to perform photosynthesis, whereas variations in other proteins (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and ribose-5-phosphate isomerase) suggest an increase of carbon fixation and decrease of carbohydrate metabolism reactions in plants exposed to pure MC-LR and cyanobacterial extracts, respectively. MC-LR was found in roots (1635.21 μg/kg fw), green tomatoes (5.15–5.41 μg/kg fw), mature tomatoes (10.52–10.83 μg/kg fw), and leaves (12,298.18 μg/kg fw). The results raise concerns relative to food safety and point to the necessity of monitoring the bioaccumulation of water toxins in agricultural systems affected by cyanotoxin contamination.
Keap1 moderates the transcription of virus induced genes through G9a-GLP and NFкB p50 recruitment, and H3K9me2 deposition (2022)

Abstract Cells must moderate transcription that is induced by virus infection to mitigate deleterious consequences of inflammation. We investigated the mechanisms whereby Keap1 moderates the transcription of genes that are induced by Sendai virus infection in mouse embryo fibroblasts (MEFs). Virus infection induced Keap1 to bind Ifnb1, Tnf and Il6 , and reduced Keap1 binding at Cdkn1a and Ccng1 . Keap1 was required for G9a and GLP to bind and to deposit H3K9me2 at these genes upon virus infection. Keap1 moderated the transcription of genes that were induced by virus infection in concert with G9a, GLP, and NFкB p50 recruitment. G9a-GLP lysine methyltransferase activity was required for Keap1 to moderate the transcription of virus induced genes. G9a-GLP inhibitors enhanced the transcription of virus induced genes, and they augmented Keap1 and NFкB p50 recruitment, in parallel with the inhibition of H3K9me2 deposition. The interdependent effects of Keap1 and G9a-GLP on transcription and on the recruitment of each other constitute a feedback circuit that moderates the transcription of virus induced genes. G9a-GLP inhibitors augmented Keap1 binding to different genes in virus infected and in uninfected MEFs, whereas they inhibited H3K9me2 deposition that was induced by virus infection selectively. G9a-GLP inhibitors stabilized Keap1 retention in permeabilized MEFs and augmented Keap1 binding to specific genes in parallel. Keap1 was required for NFкB p50 recruitment, and for the augmentation of NFкB binding by G9a-GLP inhibitors. Keap1 and the electrophile tBHQ attenuated virus induced gene transcription through independent mechanisms, and they regulated the recruitment of different NFкB subunits. Importance Excess and maladaptive immune responses to virus infections are a major contributing factor to the morbidity and mortality of COVID-19 and other diseases. Conversely, inadequate immune responses to vaccines and pathogens by individuals with suppressed immune function expose them to infections. Currently available drugs that enable therapeutic management of immune responses have low specificity and can blunt beneficial immune functions. The molecular mechanisms that moderate the transcription of genes that are induced by virus infection are incompletely understood. Characterization of the mechanisms whereby Keap1, G9a-GLP and NFкB p50 moderate virus induced gene transcription in mouse embryo fibroblasts represents the first step toward the identification of new targets for therapeutic agents that can modulate immune responsiveness.
Antigen Delivery by Lipid-Enveloped PLGA Microparticle Vaccines Mediated by in Situ Vesicle Shedding (2014)

Lipid-coated poly(lactide-co-glycolide) microparticles (LCMPs) consist of a solid polymer core wrapped by a surface lipid bilayer. Previous studies demonstrated that immunization with LCMPs surface-decorated with nanograms of antigen elicit potent humoral immune responses in mice. However, the mechanism of action for these vaccines remained unclear, as LCMPs are too large to drain efficiently to lymph nodes from the vaccination site. Here, we characterized the stability of the lipid envelope of LCMPs and discovered that in the presence of serum the lipid coating of the particles spontaneously delaminates, shedding antigen-displaying vesicles. Lipid delamination generated 180 nm liposomes in a temperature- and lipid/serum-dependent manner. Vesicle shedding was restricted by inclusion of high-TM lipids or cholesterol in the LCMP coating. Administration of LCMPs bearing stabilized lipid envelopes generated weaker antibody responses than those of shedding-competent LCMPs, suggesting that in situ release of antigen-loaded vesicles plays a key role in the remarkable potency of LCMPs as vaccine adjuvants.
Genomic methods in profiling DNA accessibility and factor localization (2019)

Recent advancements in next-generation sequencing technologies and accompanying reductions in cost have led to an explosion of techniques to examine DNA accessibility and protein localization on chromatin genome-wide. Generally, accessible regions of chromatin are permissive for factor binding and are therefore hotspots for regulation of gene expression; conversely, genomic regions that are highly occupied by histone proteins are not permissive for factor binding and are less likely to be active regulatory regions. Identifying regions of differential accessibility can be useful to uncover putative gene regulatory regions, such as enhancers, promoters, and insulators. In addition, DNA-binding proteins, such as transcription factors that preferentially bind certain DNA sequences and histone proteins that form the core of the nucleosome, play essential roles in all DNA-templated processes. Determining the genomic localization of chromatin-bound proteins is therefore essential in determining functional roles, sequence motifs important for factor binding, and regulatory networks controlling gene expression. In this review, we discuss techniques for determining DNA accessibility and nucleosome positioning (DNase-seq, FAIRE-seq, MNase-seq, and ATAC-seq) and techniques for detecting and functionally characterizing chromatin-bound proteins (ChIP-seq, DamID, and CUT&RUN). These methods have been optimized to varying degrees of resolution, specificity, and ease of use. Here, we outline some advantages and disadvantages of these techniques, their general protocols, and a brief discussion of their development. Together, these complimentary approaches have provided an unparalleled view of chromatin architecture and functional gene regulation.
Trichosporon heliocopridis sp. nov., a urease-negative basidiomycetous yeast associated with dung beetles (Heliocopris bucephalus Fabricius) (2015)

Ninety-six yeast isolates associated with dung beetles (<i>Heliocopris bucephalus</i> Fabricius) were examined based on a culture-dependent method. A comparison of the colony morphology and PCR-fingerprints obtained by (GTG)<sub>5</sub> microsatellite-primed PCR indicated that 84 of these isolates belonged to one group. Five strains (DD1-1<sup>T</sup>, DD2-33, DD4-11, DD5-15 and DD6-1) were selected as the representatives of this main group, where each of the five selected strains had been derived from a different dung beetle collected in northern Thailand. A comparison of the D1/D2 domain sequence of the large subunit rRNA gene (LSU D1/D2) and the internal transcribed spacer (ITS) sequences revealed that these five strains were the same and were related to the genus <i>Trichosporon.</i> Phylogenetic analysis based on the LSU D1/D2 plus ITS sequences placed this group within the <i>Trichosporon brassicae</i> clade, but it was clearly separated from any known species. In addition, physiological tests showed that this group had the unusual property of the inability to hydrolyse urea, which was distinctly different from the related taxon. Therefore a novel yeast species named <i>Trichosporon heliocopridis</i> sp. nov. (ex-type strain DD1-1<sup>T</sup> = TISTR 5946<sup>T</sup> = JCM 30786<sup>T</sup> = CBS 14168<sup>T</sup>) is proposed. The MycoBank number is MB812098.
Acute and regressive encephalopathy coincident with transient isolation of human immunodeficiency virus from cerebrospinal fluid of a seropositive man. (1988)

We observed the development of an acute encephalopathy in a healthy human immunodeficiency virus (HIV) seropositive man. HIV was isolated from cerebrospinal fluid but not from peripheral blood. Signs and symptoms resolved quickly without treatment. This viral isolate could be propagated only in blood cord lymphocytes, but not in peripheral blood T-lymphocytes or in continuous lymphoblastoid cell lines such as CEM. The absence of the virus in the patient's T-lymphocytes or infectivity of the virus for T-lymphocytes may explain the unusual presentation of HIV-associated encephalopathy without immunodeficiency in an asymptomatic carrier. Moreover, it raises the possibility that acute expression of HIV can be controlled by natural host defence mechanisms and that clinical manifestations may be reversible despite the patient's remaining seropositive.
HoVer Erasure Codes For Disk Arrays (2006)

We present a new family of XOR-based erasure codes primarily targeted for use in disk arrays. These codes have a unique data/parity layout, with both horizontal and vertical parity arrangements giving rise to the name HoVer codes. We give constructions that tolerate up to four disk failures. Though the codes are only approximately maximum distance separable (MDS), they have performance advantages over other codes at many common array sizes. In addition, they have fewer parameter constraints than many other codes which enable greater choices and flexibility in efficiency and performance trade-offs
On Coded Caching Systems with Offline Users (2022)

Coded caching is a technique that leverages locally cached contents at the users to reduce the network’s peak-time communication load. Coded caching achieves significant performance gains compared to uncoded caching schemes and is thus a promising technique to boost performance in future networks. In the original model introduced by Maddah-Ali and Niesen (MAN), a server stores multiple files and is connected to multiple cache-aided users through an error-free shared link; once the local caches have been filled and all users have sent their demand to the server, the server can start sending coded multicast messages to satisfy all users’ demands. A practical limitation of the original MAN model is that it halts if the server does not receive all users’ demands, which is the limiting case of asynchronous coded caching when the requests of some users arrive with infinite delay. This paper formally defines a coded caching system where some users are offline. Achievable and converse bounds are proposed for this novel setting and shown to meet under certain conditions; otherwise, they are within a constant multiplicative gap of two. Interestingly, when optimality can be be shown, the optimal load-memory tradeoff only depends on the number active users, and not on the total (active plus offline) number of users.
Recent QCD Results from ATLAS (2014)

Recent QCD results from ATLAS taken at 7 TeV center-of-mass energy using the LHC are presented, including: dijet production, isolated photon production, isolated photon production associated with jets, jet shapes in top-quark pair events, the production cross-section of the phi(1020) meson, and underlying event in jet events. Good agreement with theory predictions is seen, in particular with those made by next-to-leading-order generators. These measurements highlight the importance of precision QCD measurements for improving state-of-the-art theoretical tools and searching for new physics.
Dynamics of helping behavior and cooperation across culture (2012)

Prior research shows variation in helping behavior across culture due to cultural differences in values, perceptions, and motivations [12]. Our study extends on past research by examining how culture and fusion with one's culture influences helping behavior (help request and help given) when interacting with a cooperative versus non-cooperative counterpart. Canadian, Chinese and Indian participants engaged in an intracultural dyadic interaction using a virtual decision making game, FireSim, where they had to protect their village and its assets from seasonal fires with the option of requesting help and/or providing help to a neighboring village (counterpart). The results illustrate that Canadians (individualists) were less influenced by the situation, as their helping behavior was not significantly affected by partner's helping behavior, compared to Chinese and Indian individuals (collectivists). Moreover, Canadians were less likely to request for help but overall received more help compared to individuals from collectivistic cultures. We also found that the more a person was fused with his or her culture, the more likely that individual would provide help, if partner was cooperative. Potential implications and further research for inter-cultural helping behavior is discussed.
Importance of Smoking for Chlamydia pneumoniae Seropositivity (1994)

The results provide evidence of an association between smoking and C. pneumoniae seropositivity in the general population. The higher prevalence of smoking in men does not explain the C. pneumoniae antibody prevalence in men compared with women.
Mechanism of Action of NB2001 and NB2030, Novel Antibacterial Agents Activated by β-Lactamases (2004)

Two potent antibacterial agents designed to undergo enzyme-catalyzed therapeutic activation were evaluated for their mechanisms of action. The compounds, NB2001 and NB2030, contain a cephalosporin with a thienyl (NB2001) or a tetrazole (NB2030) ring at the C-7 position and are linked to the antibacterial triclosan at the C-3 position. The compounds exploit beta-lactamases to release triclosan through hydrolysis of the beta-lactam ring. Like cephalothin, NB2001 and NB2030 were hydrolyzed by class A beta-lactamases (Escherichia coli TEM-1 and, to a lesser degree, Staphylococcus aureus PC1) and class C beta-lactamases (Enterobacter cloacae P99 and E. coli AmpC) with comparable catalytic efficiencies (k(cat)/K(m)). They also bound to the penicillin-binding proteins of S. aureus and E. coli, but with reduced affinities relative to that of cephalothin. Accordingly, they produced a cell morphology in E. coli consistent with the toxophore rather than the beta-lactam being responsible for antibacterial activity. In biochemical assays, they inhibited the triclosan target enoyl reductase (FabI), with 50% inhibitory concentrations being markedly reduced relative to that of free triclosan. The transport of NB2001, NB2030, and triclosan was rapid, with significant accumulation of triclosan in both S. aureus and E. coli. Taken together, the results suggest that NB2001 and NB2030 act primarily as triclosan prodrugs in S. aureus and E. coli.