gebhart/patrepeval huggingface dataset:
Abstract LB-183: Sensitivity of cancer cells to oncolytic viruses is defined by IWS1 phosphorylation dependent epigenetic regulation of U2AF2 splicing and nucleocytoplasmic export of type I IFN transcripts (2020)

Abstract We have previously shown that phosphorylation of IWS1 by AKT (primarily AKT3) at Ser720/Thr721 promotes the binding of SETD2 to an Spt6/IWS1/Aly-Ref transcription elongation complex. This complex is bound via Spt6 to the Ser2-phosphorylated CTD of RNA Pol II. We have also shown that this results in the AKT-dependent trimethylation of Histone H3 at K36, a histone modification that contributes to the regulation of alternative splicing, and that this splicing pathway plays an important role in lung cancer. Here, we show that one of the genes targeted for alternative splicing via this mechanism is U2AF2, which encodes the splicing factor U2AF65. The predominant alternatively spliced U2AF2 transcript in cells which have lost IWS1, and in cells in which IWS1 is not phosphorylated, lacks exon 2, which encodes the SR domain of U2AF65. U2AF65 lacking the SR domain does not bind Prp19, a member of a seven-protein complex, which also contributes to RNA processing. U2AF65 and Prp19, along with the TREX complex, bind Cytoplasmic Accumulation Response Elements (CAR-E) in naturally intronless mRNAs and promotes their nucleocytoplasmic export. Examples of mRNAs whose transport is regulated by this mechanism include IFNα1, IFNβ1, HSPBP3 and c-Jun. Based on these data, we predicted that the production of type I IFNs would be dependent on IWS1 phosphorylation by AKT and that inhibition of this pathway would lead to increased sensitivity of cells to virus infection. Indeed, type I IFN production was decreased in such cells and infection with Vesicular Stomatitis Virus (VSV) was accordingly increased. In addition, whereas U2AF65 binds CAR-E elements in the RNA of type I interferons independent of IWS1 phosphorylation, the binding of Prp19 to the same RNA elements occured only in cells expressing AKT-phosphorylated IWS1. These data identify a mechanism by which AKT inhibits viral infection and suggest that inhibition of the AKT/IWS1 axis will increase the sensitivity of cancer cells to infection by oncolytic viruses. Citation Format: Georgios I. Laliotis, Adam D. Kenney, Arturo Orlacchio, Vincenzo Coppola, Jacob S. Yount, Philip N. Tsichlis. Sensitivity of cancer cells to oncolytic viruses is defined by IWS1 phosphorylation dependent epigenetic regulation of U2AF2 splicing and nucleocytoplasmic export of type I IFN transcripts [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-183.
The effect of temperature and initial pH on biomimetic apatite coating (2008)

Abstract Bone‐like apatite coatings were prepared using a biomimetic method in a simulated body fluid (SBF). The effect of initial pH values and immersing temperatures on biomimetic apatite coating formation was studied. Three different temperatures were used in this study: 24 (room temperature), 40, and 60°C. At each temperature, SBF solutions with three different initial pHs were chosen: low, medium, and high. The total inorganic carbon (TIC) content and pH‐time profile of each coating system were recorded during the coating formation. The apatite coatings were characterized using X‐ray diffraction (XRD), field emission scanning electron microscope (FESEM), and Fourier transform infra‐red (FTIR). It has been found that SBF temperature has a great effect on the bicarbonate decomposition rate. The bicarbonate ions tend to decompose faster as the temperature increases. The decomposition of bicarbonate ions results in a pH increase in the SBF. With different initial SBF pHs, the decomposition of different amounts of bicarbonate ions is required to reach the critical pH range of apatite formation. With different amounts of bicarbonate ions in the SBF, the surface morphology of the biomimetic apatite coating formed is different. Therefore, the initial pH of the SBF solution plays a vital role in controlling the surface morphology of the biomimetic apatite coating. Also, it was found that as the SBF temperature increased, the critical pH range at which biomimetic apatite coating forms decreased. The critical pH range for the SBF prepared at 24, 40, and 60°C was 6.65–6.71, 6.55–6.65, and 6.24–6.42, respectively. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2008
Robust Minimax Probability Machine Regression (2003)

We formulate regression as maximizing the minimum probability (#) that the true regression function is within of the regression model. Our framework starts by posing regression as a binary classification problem, such that a solution to this single classification problem directly solves the original regression problem. Minimax probability machine classification (Lanckriet et al., 2002a) is used to solve the binary classification problem, resulting in a direct bound on the minimum probability # that the true regression function is within of the regression model. This minimax probability machine regression (MPMR) model assumes only that the mean and covariance matrix of the distribution that generated the regression data are known; no further assumptions on conditional distributions are required. Theory is formulated for determining when estimates of mean and covariance are accurate, thus implying robust estimates of the probability bound #. Conditions under which the MPMR regression surface is identical to a standard least squares regression surface are given, allowing direct generalization bounds to be easily calculated for any least squares regression model (which was previously possible only under very specific, often unrealistic, distributional assumptions). We further generalize these theoretical bounds to any superposition of basis functions regression model. Experimental evidence is given supporting these theoretical results.
Roadmap on biomaterials for women’s health (2022)

Abstract The application of engineering tools and techniques to studying women’s health, including biomaterials-based approaches, is a research field experiencing robust growth. Biomaterials are natural or synthetic materials used to repair or replace damaged tissues or organs or replicate an organ’s physiological function. However, in addition to in vivo applications, there has been substantial recent interest in biomaterials for in vitro systems. Such artificial tissues and organs are employed in drug discovery, functional cell biological investigations, and basic research that would be ethically impossible to conduct in living women. This Roadmap is a collection of 11 sections written by leading and up-and-coming experts in this field who review and discuss four aspects of biomaterials for women’s health. These include conditions that disproportionately but not exclusively affect women (e.g. breast cancer), conditions unique to female reproductive organs, in both non-pregnant and pregnant states, and sex differences in non-reproductive tissues (e.g. the cardiovascular system). There is a strong need to develop this exciting field, with the potential to materially influence women’s lives worldwide.
Automated High-Throughput Synthesis of Artificial Glycopeptides. Small-Molecule Probes for Chemical Glycobiology (2002)

A fully automated method for the synthesis of artificial glycopeptides having two (similar or different) carbon-linked glycosyl moieties on a dipeptide scaffold has been developed. By use of this approach that combines the diversity of peptide/pseudopeptide and glycosides, different glycoside moieties can be incorporated onto the peptide/pseudopeptide backbone in a highly controlled manner. The approach utilizes a stepwise reductive amination with glycoside aldehyde derivatives (model 1) or (ii) glycoside reductive amination followed by glycoside amide bond formation (model 2). Further, an automated method has been utilized in the high-throughput library synthesis of 4 x 96 artificial glycopeptides. These libraries were tested as chemical probes/inhibitors of enzyme systems that convert a glucose moiety into rhamnose prior to incorporation of the rhamnose unit and the conversion of UDP-galactopyranose to UDP-galactofuranose via UDP-galactopyranose mutase enzyme during the biosynthesis of the mycobacterium cell wall.
Intracranial and Cerebral Perfusion Pressure Thresholds Associated With Inhospital Mortality Across Pediatric Neurocritical Care* (2020)

We identified mean intracranial pressure thresholds, utilizing receiver operating characteristic and regression analyses, associated with inhospital mortality that is below current guidelines-based treatment targets in both traumatic brain injury and nontraumatic brain injury patients, and age-dependent cerebral perfusion pressure thresholds associated with inhospital mortality that were above current guidelines-based targets in traumatic brain injury patients. Further study is warranted to identify data-driven intracranial pressure and cerebral perfusion pressure targets in children undergoing intracranial pressure monitoring, whether for traumatic brain injury or other indications.
PRECIP: Towards Practical and Retrofittable Confidential Information Protection. (2008)

A grand challenge in information protection is how to preserve the confidentiality of sensitive information under spyware surveillance. This problem has not been well addressed by the existing access-control mechanisms which cannot prevent the spyware already in a system from monitoring an authorized party’s interactions with sensitive data. Our answer to this challenge is PRECIP, a new security policy model which takes a first step towards practical and retrofittable confidential information protection. This model is designed to offer efficient online protection for commercial applications and operating systems. It intends to be retrofitted to these applications and systems without modifying their code. To this end, PRECIP addresses several practical issues critical to containing spyware surveillance, which however are not well handled by the previous work in access control and information-flow security. Examples include the models for human input devices such as keyboard whose sensitivity level must be dynamically determined, other shared resources such as clipboard and screen which must be accessed by different processes, and the multitasked processes which work on public and sensitive data concurrently. We applied PRECIP to Windows XP to protect the applications for editing or viewing sensitive documents and browsing sensitive websites. We demonstrate that our implementation works effectively against a wide spectrum of spyware, including keyloggers, screen grabbers and file stealers. We also evaluated the overheads of our technique, which are shown to be very small. 1
Halobacterial Rhodopsins (1999)

Following the discovery of the bacteriorhodopsin proton pump in Halobacterium halobium (salinarum), not only the halorhodopsin halide pump and two photosensor rhodopsins (sensory rhodopsin and phoborhodopsin) in the same species, but also homologs of these four rhodopsins in strains of other genera of Halobacteriaceae have been reported. Twenty-eight full (and partial) sequences of the genomic DNA of these rhodopsins have been analyzed. The deduced amino acid sequences have led to new strategies and tactics for understanding bacterial rhodopsins on a comparative basis, as summarized briefly in this article. The data discussed include (i) alignment of the sequences to qualify/characterize the conserved residues; (ii) assignment of residues that cause differences in function(s)/properties; and (iii) phylogeny of the halobacterial rhodopsins to suggest their evolutionary paths. The four kinds of rhodopsin in each strain are assumed, on the basis of their genera-specific distributions, to have arisen by at least two gene-duplication processes during evolution prior to generic speciation. The first duplication of the rhodopsin ancestor gene yielded two genes, each of which was duplicated again to give four genes in the ancestor halobacterium. The bacterium carrying four rhodopsin genes, after accumulating mutations, became ready for generic speciation and the delivery of four rhodopsins to each species. The original rhodopsin ancestor is speculated to be closest to the proton pump (bacteriorhodopsin).
CSI-EPT: A novel contrast source approach to MRI based electric properties tomography and patient-specific SAR (2013)

In this paper, we present a novel method (Contrast Source Inversion - Electric Properties Tomography or CSI-EPT) to dielectric imaging of biological tissue using so-called B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> data measurable by Magnetic Resonance Imaging (MRI) systems. Integral representations for the electromagnetic field quantities are taken as a starting point and we follow an iterative contrast source inversion approach to retrieve the dielectric tissue parameters from measured field data. Numerical results illustrate the performance of the method and show that reliable results are produced near tissue boundaries as opposed to the currently used methods. Fine structures can be resolved as well and since CSI-EPT reconstructs the electric field strength inside a scanning region of interest, it is also a promising candidate to determine the patient-specific SAR deposition during an MRI scan.
Oxidative Approach to Carbazoles and Related Compounds Using MoCl5 (2014)

Key words molybdenum - titanium - oxidative coupling - carbazoles
Finding pathogenicity islands and gene transfer events in genome data (2000)

Software and numerical results (profiles, scalograms, high and low frequency components) for all the genome sequences analyzed are available upon request from the authors.
Saturated Imaging for Inspecting Transparent Aesthetic Defects in a Polymeric Polarizer with Black and White Stripes (2018)

Machine vision systems have been widely used in industrial production lines because of their automation and contactless inspection mode. In polymeric polarizers, extremely slight transparent aesthetic defects are difficult to detect and characterize through conventional illumination. To inspect such defects rapidly and accurately, a saturated imaging technique was proposed, which innovatively uses the characteristics of saturated light in imaging by adjusting the light intensity, exposure time, and camera gain. An optical model of defect was established to explain the theory by simulation. Based on the optimum experimental conditions, active two-step scanning was conducted to demonstrate the feasibility of this detection scheme, and the proposed method was found to be efficient for real-time and in situ inspection of defects in polymer films and products.
A CREW EXPOSURE STUDY. VOLUME I. OFFSHORE (1982)

An assessment of worker exposure to potentially hazardous gases, vapors, mists, and dusts in the marine bulk liquid transportation industry is provided. Methodology for characterizing occupational exposures of crewmen to cargo- and noncargo-related materials during vessel operations in port and at sea was established. The major elements of the project included (1) a background study, (2) development of an experimental plan, and (3) trial implementation of the plan on one test at sea. The background study consisted of a search of the open literature and discussions with international maritime organizations for relevant industrial hygiene/occupational health study data. Also, two round-trip voyages aboard a product tanker and a gasoline carrier were conducted to document sources which may pose potential inhalation or dermal exposures. The background study was used to develop an experimental plan for characterizing the occupational exposures aboard bulk liquid carrier. Ten voyages were identified as necessary to reflect a representative data base covering variations in equipment, procedures, and cargos. The experimental plan was implemented in the Deck Department on one voyage of a chemical carrier.
Upregulation of Calcium Homeostasis Modulators in Contractile-To-Proliferative Phenotypical Transition of Pulmonary Arterial Smooth Muscle Cells (2021)

Excessive pulmonary artery (PA) smooth muscle cell (PASMC) proliferation and migration are implicated in the development of pathogenic pulmonary vascular remodeling characterized by concentric arterial wall thickening and arteriole muscularization in patients with pulmonary arterial hypertension (PAH). Pulmonary artery smooth muscle cell contractile-to-proliferative phenotypical transition is a process that promotes pulmonary vascular remodeling. A rise in cytosolic Ca<sup>2+</sup> concentration [(Ca<sup>2+</sup>) <sub><i>cyt</i></sub> ] in PASMCs is a trigger for pulmonary vasoconstriction and a stimulus for pulmonary vascular remodeling. Here, we report that the calcium homeostasis modulator (CALHM), a Ca<sup>2+</sup> (and ATP) channel that is allosterically regulated by voltage and extracellular Ca<sup>2+</sup>, is upregulated during the PASMC contractile-to-proliferative phenotypical transition. Protein expression of CALHM1/2 in primary cultured PASMCs in media containing serum and growth factors (proliferative PASMC) was significantly greater than in freshly isolated PA (contractile PASMC) from the same rat. Upregulated CALHM1/2 in proliferative PASMCs were associated with an increased ratio of pAKT/AKT and pmTOR/mTOR and an increased expression of the cell proliferation marker PCNA, whereas serum starvation and rapamycin significantly downregulated CALHM1/2. Furthermore, CALHM1/2 were upregulated in freshly isolated PA from rats with monocrotaline (MCT)-induced PH and in primary cultured PASMC from patients with PAH in comparison to normal controls. Intraperitoneal injection of CGP 37157 (0.6 mg/kg, q8H), a non-selective blocker of CALHM channels, partially reversed established experimental PH. These data suggest that CALHM upregulation is involved in PASMC contractile-to-proliferative phenotypical transition. Ca<sup>2+</sup> influx through upregulated CALHM1/2 may play an important role in the transition of sustained vasoconstriction to excessive vascular remodeling in PAH or precapillary PH. Calcium homeostasis modulator could potentially be a target to develop novel therapies for PAH.
Clonal dissemination of invasive and colonizing clonal complex 1 of serotype VI group B Streptococcus in central Taiwan (2014)

CC1 dissemination of serotype VI GBS thus emerges as an important invasive pathogen in infants and nonpregnant adults in central Taiwan. Serotype prevalence of GBS must be continuously monitored geographically to guide prevention strategy of GBS vaccines.
Faculty Opinions recommendation of A human gut microbial gene catalogue established by metagenomic sequencing. (2010)

To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively. PMID: 20203603 Funding information This work was supported by: Wellcome Trust, United Kingdom Grant ID: 085775
The Domain Mismatch Problem in the Broadcast Speaker Attribution Task (2021)

The demand of high-quality metadata for the available multimedia content requires the development of new techniques able to correctly identify more and more information, including the speaker information. The task known as speaker attribution aims at identifying all or part of the speakers in the audio under analysis. In this work, we carry out a study of the speaker attribution problem in the broadcast domain. Through our experiments, we illustrate the positive impact of diarization on the final performance. Additionally, we show the influence of the variability present in broadcast data, depicting the broadcast domain as a collection of subdomains with particular characteristics. Taking these two factors into account, we also propose alternative approximations robust against domain mismatch. These approximations include a semisupervised alternative as well as a totally unsupervised new hybrid solution fusing diarization and speaker assignment. Thanks to these two approximations, our performance is boosted around a relative 50%. The analysis has been carried out using the corpus for the Albayzín 2020 challenge, a diarization and speaker attribution evaluation working with broadcast data. These data, provided by Radio Televisión Española (RTVE), the Spanish public Radio and TV Corporation, include multiple shows and genres to analyze the impact of new speech technologies in real-world scenarios.
Mitochondrial Dynamics: A Key Role in Neurodegeneration and a Potential Target for Neurodegenerative Disease (2021)

In neurodegenerative diseases, neurodegeneration has been related to several mitochondrial dynamics imbalances such as excessive fragmentation of mitochondria, impaired mitophagy, and blocked mitochondria mitochondrial transport in axons. Mitochondria are dynamic organelles, and essential for energy conversion, neuron survival, and cell death. As mitochondrial dynamics have a significant influence on homeostasis, in this review, we mainly discuss the role of mitochondrial dynamics in several neurodegenerative diseases. There is evidence that several mitochondrial dynamics-associated proteins, as well as related pathways, have roles in the pathological process of neurodegenerative diseases with an impact on mitochondrial functions and metabolism. However, specific pathological mechanisms need to be better understood in order to propose new therapeutic strategies targeting mitochondrial dynamics that have shown promise in recent studies.
Comment on the Comparison of Measured and Calculated Values of Ion Aerosol Attachment Coefficients (1989)

A recent paper by Pui at al. (1988) presents measurements of the attachment coefficients for ions to uncharged aerosol particles as a function of size. This paper is important because it gives an absolute measurement of the coefficients with which to test theoretical results which are now being used in lieu of measurements