gebhart/patrepeval huggingface dataset:
Histone Hyperacetylation Occurs on Promoters of Lytic Cycle Regulatory Genes in Epstein-Barr Virus-Infected Cell Lines Which Are Refractory to Disruption of Latency by Histone Deacetylase Inhibitors (2008)

Activation of the Epstein-Barr virus (EBV) lytic cycle is mediated through the combined actions of ZEBRA and Rta, the products of the viral BZLF1 and BRLF1 genes. During latency, these two genes are tightly repressed. Histone deacetylase inhibitors (HDACi) can activate viral lytic gene expression. Therefore, a widely held hypothesis is that Zp and Rp, the promoters for BZLF1 and BRLF1, are repressed by chromatin and that hyperacetylation of histone tails, by allowing the access of positively acting factors, leads to transcription of BZLF1 and BRLF1. To investigate this hypothesis, we used chromatin immunoprecipitation (ChIP) to examine the acetylation and phosphorylation states of histones H3 and H4 on Zp and Rp in three cell lines, Raji, B95-8, and HH514-16, which differ in their response to EBV lytic induction by HDACi. We studied the effects of three HDACi, sodium butyrate (NaB), trichostatin A (TSA), and valproic acid (VPA). We also examined the effects of tetradecanoyl phorbol acetate (TPA) and 5-aza-2'-deoxycytidine, a DNA methyltransferase inhibitor, on histone modification. In Raji cells, TPA and NaB act synergistically to activate the EBV lytic cycle and promote an increase in histone H3 and H4 acetylation and phosphorylation at Zp and Rp. Surprisingly, however, when Raji cells were treated with NaB or TSA, neither of which is sufficient to activate the lytic cycle, an increase of comparable magnitude of hyperacetylated and phosphorylated histone H3 at Zp and Rp was observed. In B95-8 cells, NaB inhibited lytic induction by TPA, yet NaB promoted hyperacetylation of H3 and H4. In HH514-16 cells, NaB and TSA strongly activated the EBV lytic cycle and caused hyperacetylation of histone H3 on Zp and Rp. However, when HH514-16 cells were treated with VPA, lytic cycle mRNAs or proteins were not induced, although histone H3 was hyperacetylated as measured by immunoblotting or by ChIP on Zp and Rp. Taken together, our data suggest that open chromatin at EBV BZLF1 and BRLF1 promoters is not sufficient to activate EBV lytic cycle gene expression.
Reanalysis of Some Baboon Descent Data (1976)

Wagner and Altmann [1973] recently reported an analysis of a set of baboon descent times, some of which were left censored due to varying arrival times at the observation site. Any transformation of the data which reverses order produced a set of right censored observations. In this way, the Kaplan-Meier [1958] estimate of the descent time distribution can be computed. Estimates of the mean and variance of the distribution are given, as well as the standard error of the estimate of the mean.
A Strategy for Automatically Extracting References from PDF Documents (2012)

Every day the number of citations an author receives is becoming more important than the size of his list of publications. The automatic extraction of bibliographic references in scientific articles is still a difficult problem in Document Engineering, even if the document is originally in digital form. This paper presents a strategy for extracting references of scientific documents in PDF format. The scheme proposed was validated in Live Memory platform, developed to generate digital libraries of proceedings of technical events.
Transformation of low-molecular linear caprolactam oligomers by the caprolactam-degrading bacterium Pseudomonas putida BS394(pBS268) (2010)

A biosensor based on the most active caprolactam-degrading strain Pseudomonas putida BS394(pBS268) was used in the study of aerobic degradation of linear caprolactam oligomers by bacterial cells. The changes in the respiratory activity of the strain depend quantitatively on caprolactam dimer concentration, making it possible to develop biosensors for detection of caprolactam oligomers in aqueous media. Based on mass spectrometry data, the scheme of transformation of linear caprolactam oligomers by the degrader strain P. putida BS394(pBS268) was proposed for the first time. It was found that oxidative transamination to respective dicarbonic acids may be one of the mechanisms of transformation of linear caprolactam oligomers. According to the scheme proposed, the ability of the caprolactam-degrading strain to transform linear oligomers results from the broad substrate specificities of two enzymes of the caprolactam degradation pathway: 2-oxoglutarate-6-aminohexanoate transaminase and 6-oxohexanoate dehydrogenase. Transformation of linear oligomers is genetically controlled by the CAP biodegradation plasmid pBS268.
Low Mortality and High Morbidity in Severe Acute Pancreatitis Without Organ Failure: A Case for Revising the Atlanta Classification to Include “Moderately Severe Acute Pancreatitis” (2009)

Patients with SAP and NOF have prolonged hospitalizations but low mortality. The Atlanta classification should be revised to include a patient group defined as "moderately severe acute pancreatitis" that identifies those patients currently classified as SAP without OF.
Reproduction of a plane-wave sound field using an array of loudspeakers (2001)

Reproduction of a sound field is a fundamental problem in acoustic signal processing. In this paper, we use a spherical harmonics analysis to derive performance bounds on how well an array of loudspeakers can recreate a three-dimensional (3-D) plane-wave sound field within a spherical region of space. Specifically, we develop a relationship between the number of loudspeakers, the size of the reproduction sphere, the frequency range, and the desired accuracy. We also provide analogous results for the special case of reproduction of a two-dimensional (2-D) sound field. Results are verified through computer simulations.
Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware (2019)

The revolution in low-cost consumer photography and computation provides fertile opportunity for a disruptive reduction in the cost of biomedical imaging. Conventional approaches to low-cost microscopy are fundamentally restricted, however, to modest field of view (FOV) and/or resolution. We report a low-cost microscopy technique, implemented with a Raspberry Pi single-board computer and color camera combined with Fourier ptychography (FP), to computationally construct 25-megapixel images with sub-micron resolution. New image-construction techniques were developed to enable the use of the low-cost Bayer color sensor, to compensate for the highly aberrated re-used camera lens and to compensate for misalignments associated with the 3D-printed microscope structure. This high ratio of performance to cost is of particular interest to high-throughput microscopy applications, ranging from drug discovery and digital pathology to health screening in low-income countries. 3D models and assembly instructions of our microscope are made available for open source use.
User-oriented document summarization through vision-based eye-tracking (2009)

We propose a new document summarization algorithm which is personalized. The key idea is to rely on the attention (reading) time of individual users spent on single words in a document as the essential clue. The prediction of user attention over every word in a document is based on the user's attention during his previous reads, which is acquired via a vision-based commodity eye-tracking mechanism. Once the user's attentions over a small collection of words are known, our algorithm can predict the user's attention over every word in the document through word semantics analysis. Our algorithm then summarizes the document according to user attention on every individual word in the document. With our algorithm, we have developed a document summarization prototype system. Experiment results produced by our algorithm are compared with the ones manually summarized by users as well as by commercial summarization software, which clearly demonstrates the advantages of our new algorithm for user-oriented document summarization.
A donor splice mutation and a single-base deletion produce two carboxyl-terminal variants of human serum albumin. (1991)

At least 35 allelic variants of human serum albumin have been sequenced at the protein level. All except two COOH-terminal variants, Catania and Venezia, are readily explainable as single-point substitutions. The two chain-termination variants are clustered in certain locations in Italy and are found in numerous unrelated individuals. In order to correlate the protein change in these variants with the corresponding DNA mutation, the two variant albumin genes have been cloned, sequenced, and compared to normal albumin genomic DNA. In the Catania variant, a single base deletion and subsequent frameshift leads to a shortened and altered COOH terminus. Albumin Venezia is caused by a mutation that alters the first consensus nucleotide of the 5' donor splice junction of intron 14 and the 3' end of exon 14, which is shortened from 68 to 43 base pairs. This change leads to an exon skipping event resulting in direct splicing of exon 13 to exon 15. The predicted Venezia albumin product has a truncated amino acid sequence (580 residues instead of 585), and the COOH-terminal sequence is altered after Glu-571. The variant COOH terminus ends with the dibasic sequence Arg-Lys that is apparently removed through stepwise cleavage by serum carboxypeptidase B to yield several forms of circulating albumin.
Peer-to-peer network for medical imaging (2010)

Nos últimos anos, a imagem médica em formato digital tem sido uma ferramenta cada vez mais importante quer para o diagnóstico médico quer para o auxílio ao tratamento. Assim, equipamentos de aquisição digital e repositórios de imagem médica são cada vez mais comuns em instituições de saúde, podendo até haver mais que um repositório numa instituição. No entanto, esta proliferação de repositórios leva a que a informação esteja dispersa nos vários locais. Esta dispersão da informação juntamente com as diferenças no armazenamento entre instituições são claros obstáculos à pesquisa e acesso integrado a essa informação. Esta dissertação visa o estudo da tecnologia Peer-to-Peer de forma a minimizar os problemas associados à dispersão e heterogeneidade da informação.
Evolution of an Autotransporter: Domain Shuffling and Lateral Transfer from Pathogenic Haemophilus to Neisseria (2001)

The genomes of pathogenic Haemophilus influenzae strains are larger than that of Rd KW20 (Rd), the nonpathogenic laboratory strain whose genome has been sequenced. To identify potential virulence genes, we examined genes possessed by Int1, an invasive nonencapsulated isolate from a meningitis patient, but absent from Rd. Int1 was found to have a novel gene termed lav, predicted to encode a member of the AIDA-I/VirG/PerT family of virulence-associated autotransporters (ATs). Associated with lav are multiple repeats of the tetranucleotide GCAA, implicated in translational phase variation of surface molecules. Laterally acquired by H. influenzae, lav is restricted in distribution to a few pathogenic strains, including H. influenzae biotype aegyptius and Brazilian purpuric fever isolates. The DNA sequence of lav is surprisingly similar to that of a gene previously described for Neisseria meningitidis. Sequence comparisons suggest that lav was transferred relatively recently from Haemophilus to Neisseria, shortly before the divergence of N. meningitidis and Neisseria gonorrhoeae. Segments of lav predicted to encode passenger and beta-domains differ sharply in G+C base content, supporting the idea that AT genes have evolved by fusing domains which originated in different genomes. Homology and base sequence comparisons suggest that a novel biotype aegyptius AT arose by swapping an unrelated sequence for the passenger domain of lav. The unusually mobile lav locus joins a growing list of genes transferred from H. influenzae to Neisseria. Frequent gene exchange suggests a common pool of hypervariable contingency genes and may help to explain the origin of invasiveness in certain respiratory pathogens.
Tardive Dystonia Induced by Atypical Neuroleptics: A Case Report with Olanzapine (2004)

We report the case of a 17-year-old-boy with schizophrenia who developed tardive dystonia after 9 months of treatment with olanzapine. This case and the relevant literature show that when neuroleptic treatment is indicated, switching to another atypical neuroleptic might be helpful for both tardive dystonia and schizophrenia. In such a case, clozapine appears to be the first-line therapeutic option.
A phase space model of Fourier ptychographic microscopy (2014)

A new computational imaging technique, termed Fourier ptychographic microscopy (FPM), uses a sequence of low-resolution images captured under varied illumination to iteratively converge upon a high-resolution complex sample estimate. Here, we propose a mathematical model of FPM that explicitly connects its operation to conventional ptychography, a common procedure applied to electron and X-ray diffractive imaging. Our mathematical framework demonstrates that under ideal illumination conditions, conventional ptychography and FPM both produce datasets that are mathematically linked by a linear transformation. We hope this finding encourages the future cross-pollination of ideas between two otherwise unconnected experimental imaging procedures. In addition, the coherence state of the illumination source used by each imaging platform is critical to successful operation, yet currently not well understood. We apply our mathematical framework to demonstrate that partial coherence uniquely alters both conventional ptychography’s and FPM’s captured data, but up to a certain threshold can still lead to accurate resolution-enhanced imaging through appropriate computational post-processing. We verify this theoretical finding through simulation and experiment.
A rare case of neuroleptic malignant syndrome presenting with serious hyperthermia treated with a non-invasive cooling device: a case report (2009)

Introduction: A rare side effect of antipsychotic medication is neuroleptic malignant syndrome, mainly characterized by hyperthermia, altered mental state, haemodynamic dysregulation, elevated serum creatine kinase and rigor.There may be multi-organ dysfunction including renal and hepatic failure as well as serious rhabdomyolysis, acute respiratory distress syndrome and disseminated intravascular coagulation.The prevalence of neuroleptic malignant syndrome is between 0.02% and 2.44% for patients taking neuroleptics and it is not necessary to fulfil all cardinal features characterizing the syndrome to be diagnosed with neuroleptic malignant syndrome.Because of other different life-threatening diseases matching the various clinical findings, the correct diagnosis can sometimes be hard to make.A special problem of intensive care treatment is the management of severe hyperthermia.Lowering of body temperature, however, may be a major clinical problem because hyperthermia in neuroleptic malignant syndrome is typically unresponsive to antipyretic agents while manual cooling proves difficult due to peripheral vasoconstriction.Case presentation: A 22-year-old Caucasian man was admitted unconscious with a body temperature of 42°C, elevated serum creatine phosphokinase, tachycardia and hypotonic blood pressure.In addition to intensive care standard therapy for coma and shock, a non-invasive cooling device (Arctic Sun 2000®, Medivance Inc., USA), originally designed to induce mild therapeutic hypothermia in patients after cardiopulmonary resuscitation, was used to lower body temperature.After successful treatment it became possible to obtain information from the patient about his recent ambulant treatment with Olanzapin (Zyprexa ® ) for schizophrenia. Conclusion:Numerous case reports have been published about patients who developed neuroleptic malignant syndrome due to Olanzapin (Zyprexa ® ) medication.Frequently hyperthermia has been observed in these cases with varying outcomes.In our case the only residual impairment for the patient is dysarthria with corresponding symmetric cerebellar pyramidal cell destruction demonstrated by increased signal intensity in T2-weighted magnetic resonance imaging, most likely caused by the excessive hyperthermia.
Monoclonal antibodies to CD2 and lymphocyte function-associated antigen 3 inhibit human thymic epithelial cell-dependent mature thymocyte activation. (1987)

Recent study of human thymocyte-thymic epithelial (TE) cell interactions has demonstrated that thymocytes bind to TE cells, and a consequence of this binding is the provision of accessory cell signals by TE cells for phytohemagglutinin (PHA)-induced mature thymocyte activation. In this paper we report on studies of the molecules involved in TE cell-dependent mature thymocyte activation. TE-thymocyte interactions necessary for PHA-induced thymocyte activation were inhibited by monoclonal antibodies against the cluster of differentiation (CD)2 antigen on thymocytes and lymphocyte function-associated (LFA)-3 antigen on TE cells. Inhibition of TE accessory cell signals by antibodies against CD2 (alpha CD2) and LFA-3 (alpha LFA-3) antigens occurred early on during thymocyte activation and prevented thymocyte interleukin 2 receptor expression. Further, alpha CD2 and alpha LFA-3 inhibited PHA-induced thymocyte activation in whole thymic explant cultures suggesting a significant role of the CD2 and LFA-3 antigens in thymocyte activation when accessory cell signals for PHA-induced thymocyte triggering were delivered by cells within an intact thymic microenvironment.
The N-terminal 513 amino acids of the envelope glycoprotein gB of human cytomegalovirus stimulates both B- and T-cell immune responses in humans (1991)

Host defense against human cytomegalovirus (HCMV) involves both humoral and cell-mediated immunity. In this report, human immune responses to glycoproteins encoded by the HCMV gB homolog gene have been examined by using glycoproteins purified by immunoaffinity from HCMV virions and recombinant proteins expressed by vaccinia viruses containing either the entire gB open reading frame or a C-terminal deletion mutant, gBm165, coding for the N-terminal 513 amino acids of gB. Neutralizing antibodies, helper T cells, and cytotoxic T cells reactive with epitopes on the N-terminal portion of gB were detected in some seropositive individuals, suggesting that this region of gB may be important in eliciting protective immunity during natural infection for some individuals.
Curve and surface fitting : an introduction (1986)

The purpose of this book is to reveal to the interested (but perhaps mathematically unsophisticated) user the foundations and major features of several basic methods for curve and surface fitting that are currently in use.
Heparin-binding VEGFR1 variants as long-acting VEGF inhibitors for treatment of intraocular neovascular disorders (2021)

Neovascularization is a key feature of ischemic retinal diseases and the wet form of age-related macular degeneration (AMD), all leading causes of severe vision loss. Vascular endothelial growth factor (VEGF) inhibitors have transformed the treatment of these disorders. Millions of patients have been treated with these drugs worldwide. However, in real-life clinical settings, many patients do not experience the same degree of benefit observed in clinical trials, in part because they receive fewer anti-VEGF injections. Therefore, there is an urgent need to discover and identify novel long-acting VEGF inhibitors. We hypothesized that binding to heparan-sulfate proteoglycans (HSPG) in the vitreous, and possibly other ocular structures, may be a strategy to promote intraocular retention, ultimately leading to a reduced burden of intravitreal injections. We designed a series of VEGF receptor 1 variants and identified some with strong heparin-binding characteristics and ability to bind to vitreous matrix. Our data indicate that some of our variants have longer duration and greater efficacy in animal models of intraocular neovascularization than current standard of care. Our study represents a systematic attempt to exploit the functional diversity associated with heparin affinity of a VEGF receptor.
Blood Platelets Are Assembled Principally at the Ends of Proplatelet Processes Produced by Differentiated Megakaryocytes (1999)

Megakaryocytes release mature platelets in a complex process. Platelets are known to be released from intermediate structures, designated proplatelets, which are long, tubelike extensions of the megakaryocyte cytoplasm. We have resolved the ultrastructure of the megakaryocyte cytoskeleton at specific stages of proplatelet morphogenesis and correlated these structures with cytoplasmic remodeling events defined by video microscopy. Platelet production begins with the extension of large pseudopodia that use unique cortical bundles of microtubules to elongate and form thin proplatelet processes with bulbous ends; these contain a peripheral bundle of microtubules that loops upon itself and forms a teardrop-shaped structure. Contrary to prior observations and assumptions, time-lapse microscopy reveals proplatelet processes to be extremely dynamic structures that interconvert reversibly between spread and tubular forms. Microtubule coils similar to those observed in blood platelets are detected only at the ends of proplatelets and not within the platelet-sized beads found along the length of proplatelet extensions. Growth and extension of proplatelet processes is associated with repeated bending and bifurcation, which results in considerable amplification of free ends. These aspects are inhibited by cytochalasin B and, therefore, are dependent on actin. We propose that mature platelets are assembled de novo and released only at the ends of proplatelets, and that the complex bending and branching observed during proplatelet morphogenesis represents an elegant mechanism to increase the numbers of proplatelet ends.
Connection between Polymer Molecular Weight, Density, Chain Dimensions, and Melt Viscoelastic Properties (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConnection between Polymer Molecular Weight, Density, Chain Dimensions, and Melt Viscoelastic PropertiesL. J. Fetters, D. J. Lohse, D. Richter, T. A. Witten, and A. ZirkelCite this: Macromolecules 1994, 27, 17, 4639–4647Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/ma00095a001https://doi.org/10.1021/ma00095a001research-articleACS PublicationsRequest reuse permissionsArticle Views17234Altmetric-Citations1735LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts