gebhart/patrepeval huggingface dataset:
Mechanistic Aspects of Photoinactivation of Candida albicans by Exogenous Porphyrins† (2012)

The mechanism of photoinactivation of Candida albicans by 3.5 μM uncharged, cationic or anionic porphyrins under blue light (407-420 nm) was found to be dependent on the uptake of porphyrins into yeast cells, and was also dependent on the presence or absence of proteins in the photosensitization medium. In a very protein-rich medium, a decrease in viability was observed only with the uncharged porphyrin. Photoinactivation by uncharged or cationic porphyrins in a protein-poorer medium resulted in total eradication, whereas no significant decrease was observed with the anionic porphyrin. Phototreatment in PBS resulted in eradication with all three porphyrins. X-ray microanalysis after phototreatment by the uncharged or cationic porphyrins in the protein-poor medium exhibited ion loss, indicating cell-membrane damage. Transmission electron microscopy indicated cellular and chromosomal damage. No ion loss or cell damage was observed in this medium with the anionic porphyrin. The efficiency of photoeradication of C. albicans is dependent on porphyrin uptake, which might lead (upon illumination) to processes that facilitate the formation of reactive oxygen species that damage the cells. Uptake of charged porphyrins is dependent on protein quantity and quality in the photosensitization microenvironment. This fact must be taken into account when using charged photosensitizers.
Studies of metallofullerene primary soots by laser and thermal desorption mass spectrometry (1993)

Laser desorption (LD) and thermal desorption (TD) mass spectra of the metallofullerenes found in arc-produced primary soots have been studied for a large variety of alkaline earth and lanthanide elements. The metallofullerene ratios found in the LD spectra indicate that two distinct groups are observed: Sc, Y, La, Ce, Pr, Nd, Gd, Tb, Ho, Er, and Lu (group A) and Ca, Sr, Sm, Eu, and Yb (group B). The TD spectra of most of these same soots also separate into two groups that contain the same elements as groups A and B. Group A metallofullerenes show strong signals in both LD and TD spectra. Group B metallofullerenes are distinguished by their presence in the LD spectra but absence in the TD spectra. From the general ionic behavior of the elements of these groups, and recent studies of the endohedral oxidation states, we propose that the oxidation states are +3 for group A and +2 for group B. C70 metallofullerenes are anomalous in that they are absent in TD spectra for all group A and B elements, even at T = 750-degrees-C, but present in LD spectra.
HLA‐DQ antigens and DQβ amino acid 57 of Japanese patients with insulin‐dependent diabetes mellitus: detection of a DRw8DQw8 haplotype (1989)

DQw8 (DQw3.2) on DR4 haplotypes is a susceptibility gene for development of insulin-dependent diabetes mellitus (IDDM) in Caucasoids, possibly because it encodes a non-Asp amino acid (aa) (i.e. Ala) at residue 57 of the DQ beta chain (non-Asp-57). Most Caucasoid IDDM patients are homozygous non-Asp-57. We have examined 14 Japanese IDDM patients, selected to be either DR4 or DRw9 (associated to IDDM among Japanese). Their DQB1 alleles and the aa encoded by their DQB1 codons 57 were identified, using 11 different sequence-specific oligonucleotide probes. Secondly, they were examined with DQw8 specific T lymphocyte clones and with anti-DQ monoclonal antibodies. The DQB1 genes on their DR4 and DRw9 haplotypes in all cases encoded Asp-57. Two patients were Asp-57 homozygous, the rest were Asp-57/non-Asp-57 heterozygous. The DR4 haplotypes all carried DQw4 (rather than DQw8), and the DRw9 haplotypes all carried DQw9. Furthermore, five of six DRw8 positive patients carried a previously undetected DRw8DQw8 haplotype, where both the DQA1 and DQB1 genes were similar to those usually found on the DR4DQw8 haplotype. Thus, the DR/DQ allele combinations and aa residue 57 of the DQ beta chain of Caucasoid and Japanese IDDM patients are largely different.
Abstract WP282: Moyamoya Disease and Pregnancy: A Single Institutional Experience in the USA (2018)

Introduction: Moyamoya disease is a progressive bilateral steno-occlusive disease of the terminal internal carotid arteries accompanied by development of collateral moyamoya vessels. It affects a younger population and thus, women in their reproductive years. We aim to define the practices, comorbidities and outcomes of pregnancies in women with moyamoya disease. Method: We conducted a retrospective review of 33 patients and 49 successful pregnancies between 1992 and 2017 at Stanford Health Care/Lucile Packard Children’s Hospital from our institutional database by surveys and chart review. Results: To date we have completed 1483 revascularization procedures in 930 patients. Out of these 930 patients we identified 45 patients who had pregnancies immediately prior to the diagnosis of moyamoya disease and some after being diagnosed with moyamoya. 33 out of these 45 patients’ charts and consents were available for review. These 33 patients had 49 successful pregnancies. There were 20 single pregnancies, 10 women had 2 pregnancies each and 3 woman had 3 successful pregnancies. 22 pregnancies were NVD (normal vaginal deliveries), 2 were assisted vaginal and 25 were C-sections. Maternal age varied from 19 years to 40 years. Gestational age ranged between 32 weeks to 40 weeks. 8/49(16.3%) pregnancies were associated with transient ischemic attacks or stroke. 44 pregnancies had a history of revascularization before or during pregnancy, and 5 pregnancies occurred prior to any revascularization. 8/49(16.3%) pregnancies were associated with eclampcia and pre-eclampcia and 9/49(18%) with hypertension. Neonatal complications included low birth weight 2/49 (4%), Mild jaundice 2/49 (4%), Tachypnea 1/49 (2%), Acid reflux 1/49 (2%), NICU stay 3/49 (6%). Conclusion: Our study shows that the trend in the USA is towards vaginal delivery in patients with moyamoya disease: 51.1%, is less than whein compared with studies in Asia. We also show that both the patients and babies do well. The complication rate is minimal, including no strokes in the peripartum period in patients who have been treated. We would advocate vaginal deliveries in the absence of any other contraindications along with peripartum blood pressure control.
A tribute to Dr. Gordon Hisashi Sato (December 24, 1927–March 31, 2017) (2018)

Gordon H. Sato, an innovator in mammalian tissue culture and integrated cellular physiology, passed away in 2017. In tribute to Dr. Sato, In Vitro Cellular and Developmental Biology-Animal presents a collection of invited remembrances from six colleagues whose associations with Dr. Sato spanned more than 40 years. Dr. Sato was a past president of the Tissue Culture Association (now the Society for In Vitro Biology), editor-in-chief of In Vitro Cellular and Developmental Biology (1987-1991), and the recipient of the lifetime achievement award from the Society for In Vitro Biology (2002). He was elected to the US National Academy of Sciences in 1984.
Suppression of antigen-specific adaptive immunity by IL-37 via induction of tolerogenic dendritic cells (2014)

IL-1 family member IL-37 limits innate inflammation in models of colitis and LPS-induced shock, but a role in adaptive immunity remains unknown. Here, we studied mice expressing human IL-37b isoform (IL-37tg) subjected to skin contact hypersensitivity (CHS) to dinitrofluorobenzene. CHS challenge to the hapten was significantly decreased in IL-37tg mice compared with wild-type (WT) mice (-61%; P < 0.001 at 48 h). Skin dendritic cells (DCs) were present and migrated to lymph nodes after antigen uptake in IL-37tg mice. When hapten-sensitized DCs were adoptively transferred to WT mice, antigen challenge was greatly impaired in mice receiving DCs from IL-37tg mice compared with those receiving DCs from WT mice (-60%; P < 0.01 at 48 h). In DCs isolated from IL-37tg mice, LPS-induced increase of MHC II and costimulatory molecule CD40 was reduced by 51 and 31%, respectively. In these DCs, release of IL-1β, IL-6, and IL-12 was reduced whereas IL-10 secretion increased (37%). Consistent with these findings, DCs from IL-37tg mice exhibited a lower ability to stimulate syngeneic and allogeneic naive T cells as well as antigen-specific T cells and displayed enhanced induction of T regulatory (Treg) cells (86%; P < 0.001) in vitro. Histological analysis of CHS skin in mice receiving hapten-sensitized DCs from IL-37tg mice revealed a marked reduction in CD8(+) T cells (-74%) but an increase in Treg cells (2.6-fold). Together, these findings reveal that DCs expressing IL-37 are tolerogenic, thereby impairing activation of effector T-cell responses and inducing Treg cells. IL-37 thus emerges as an inhibitor of adaptive immunity.
‘Template-switching’: a supramolecular strategy for the quantitative, gram-scale construction of a molecular target in the solid state (2003)

A template–switching strategy based on the modularity of template-directed solid-state synthesis has been successfully utilised to achieve a quantitative, stereospecific solid-state synthesis of a p-[2.2]-cyclophane target in gram quantities.
Architecture of Intact Natural Human Plaque Biofilms Studied by Confocal Laser Scanning Microscopy (2000)

Determination of the structure of human plaque will be of great benefit in the prediction of its formation and also the effects of treatment. However, a problem lies in the harvesting of undisturbed intact plaque samples from human volunteers and the viewing of the biofilms in their natural state. In this study, we used an in situ device for the in vivo generation of intact dental plaque biofilms on natural tooth surfaces in human subjects. Two devices were placed in the mouths of each of eight healthy volunteers and left to generate biofilm for 4 days. Immediately upon removal from the mouth, the intact, undisturbed biofilms were imaged by the non-invasive technique of confocal microscopy in both reflected light and fluorescence mode. Depth measurements indicated that the plaque formed in the devices was thicker round the edges at the enamel/nylon junction (range = 75-220 microm) than in the center of the devices (range = 35-215 microm). The reflected-light confocal images showed a heterogeneous structure in all of the plaque biofilms examined; channels and voids were clearly visible. This is in contrast to images generated previously by electron microscopy, suggesting a more compact structure. Staining of the biofilms with fluorescein in conjunction with fluorescence imaging suggested that the voids were fluid-filled. This more open architecture is consistent with recent models of biofilm structure from other habitats and has important implications for the delivery of therapeutics to desired targets within the plaque.
Multi-Party Secret Key Agreement Over State-Dependent Wireless Broadcast Channels (2016)

We consider a group of m trusted and authenticated nodes that aim to create a shared secret key K over a wireless channel in the presence of an eavesdropper Eve. We assume that there exists a state-dependent wireless broadcast channel from one of the honest nodes to the rest of them including Eve. All of the trusted nodes can also discuss over a cost-free, noiseless and unlimited rate public channel which is also overheard by Eve. For this setup, we develop an information-theoretically secure secret key agreement protocol. We show the optimality of this protocol for “linear deterministic” wireless broadcast channels. This model generalizes the packet erasure model studied in the literature for wireless broadcast channels. Here, the main idea is to convert a deterministic channel into multiple independent erasure channels by using superposition coding. For “state-dependent Gaussian” wireless broadcast channels, by using insights from the deterministic problem, we propose an achievability scheme based on a multi-layer wiretap code. By using the wiretap code, we can mimic the phenomenon of converting the wireless channel into multiple independent erasure channels. Then, finding the best achievable secret key generation rate leads to solving a non-convex power allocation problem over these channels (layers). We show that using a dynamic programming algorithm, one can obtain the best power allocation for this problem. Moreover, we prove the optimality of the proposed achievability scheme for the regime of high-SNR and large-dynamic range over the channel states in the (generalized) degrees of freedom sense.
Virtual Leashing: Internet-Based Software Piracy Protection (2005)

Software-splitting is a technique for protecting software from piracy by removing code fragments from an application and placing them on a remote trusted server. The server provides the missing functionality but never the missing code. As long as the missing functionality is hard to reverse-engineer, the application cannot run without validating itself to the server. Current software-splitting techniques scale poorly to the Internet because interactions with the remote server are synchronous: the application must frequently block waiting for a response from the server. Perceptible delays due to network latency are unacceptable for many kinds of highly-reactive applications, such as games or graphics applications. This paper introduces virtual leashing, the first non-blocking software-splitting technique. Virtual leashing ensures that the application and the server communicate asynchronously, so the application’s performance is independent (within reason) of large or variable network latencies. Experiments show that virtual leashing makes only modest demands on communication bandwidth, space, and computation.
Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences (2019)

Author: Linnér, Richard Karlsson et al.; Genre: Journal Article; Issued: 2019; Open Access; Title: Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences
Lung microenvironments harbor Mycobacterium tuberculosis phenotypes with distinct treatment responses (2023)

ABSTRACT Tuberculosis lung lesions are complex and harbor heterogeneous microenvironments that influence antibiotic effectiveness. Major strides have been made recently in understanding drug pharmacokinetics in pulmonary lesions, but the bacterial phenotypes that arise under these conditions and their contribution to drug tolerance is poorly understood. A pharmacodynamic marker called the RS ratio quantifies ongoing rRNA synthesis based on the abundance of newly-synthesized precursor rRNA relative to mature structural rRNA. Application of the RS ratio in the C3HeB/FeJ mouse model demonstrated that Mycobacterium tuberculosis populations residing in different tissue microenvironments are phenotypically distinct and respond differently to drug treatment with rifampin, isoniazid or bedaquiline. This work provides a foundational basis required to address how anatomic and pathologic microenvironmental niches may contribute to the long treatment duration and drug tolerance during treatment of human tuberculosis.
Computated Turbulent Flow In A Turnaround Duct (1991)

Kinetic energy of turbulence near wall predicted accurately. Report describes numerical simulation of two-dimensional turbulent flow in duct having 180 degree bend. Study contributes to fund of information needed to design advanced engines containing turbulent flows.
Investigation of the Species Origin of the St. Jude Porcine Lung Epithelial Cell Line (SJPL) Made Available to Researchers (2010)

The SJPL cell line was reported and described as an immortalized porcine lung epithelial cell line suitable for influenza virus replication by Seo et al. (5) and has been available to researchers through ATCC (American Type Culture Collection) cell depositary services (deposit date, 5 April 2001; assigned accession number, PTA-3256) following a material transfer agreement. Recent findings indicate that the SJPL cell line is not of porcine origin but is more likely of monkey origin.
An electrochemical investigation of the redox properties of bacteriochlorophyll and bacteriopheophytin in aprotic solvents (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn electrochemical investigation of the redox properties of bacteriochlorophyll and bacteriopheophytin in aprotic solventsTherese M. Cotton and Richard P. Van DuyneCite this: J. Am. Chem. Soc. 1979, 101, 25, 7605–7612Publication Date (Print):December 1, 1979Publication History Published online1 May 2002Published inissue 1 December 1979https://pubs.acs.org/doi/10.1021/ja00519a023https://doi.org/10.1021/ja00519a023research-articleACS PublicationsRequest reuse permissionsArticle Views218Altmetric-Citations47LEARN 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
Single‐cell sequencing and tumorigenesis: improved understanding of tumor evolution and metastasis (2017)

Extensive genomic and transcriptomic heterogeneity in human cancer often negatively impacts treatment efficacy and survival, thus posing a significant ongoing challenge for modern treatment regimens. State-of-the-art DNA- and RNA-sequencing methods now provide high-resolution genomic and gene expression portraits of individual cells, facilitating the study of complex molecular heterogeneity in cancer. Important developments in single-cell sequencing (SCS) technologies over the past 5 years provide numerous advantages over traditional sequencing methods for understanding the complexity of carcinogenesis, but significant hurdles must be overcome before SCS can be clinically useful. In this review, we: (1) highlight current methodologies and recent technological advances for isolating single cells, single-cell whole-genome and whole-transcriptome amplification using minute amounts of nucleic acids, and SCS, (2) summarize research investigating molecular heterogeneity at the genomic and transcriptomic levels and how this heterogeneity affects clonal evolution and metastasis, and (3) discuss the promise for integrating SCS in the clinical care arena for improved patient care.
Mechanical strains and stresses in aluminum and copper interconnect lines for 0.18 μm logic technologies (1999)

The mechanical stress state of conventional Al, damascene Al and damascene Cu lines of a 0.18 μm logic technology flow has been determined using a novel X-Ray diffraction method that permits measurement of stress on an array of critical-dimension lines on the product die. The mechanical stress levels in narrow RIE Al lines are small when the lines are unpassivated, but quite large (Hydrostatic stress of 537 MPa) when an inter-level dielectric (ILD) is deposited onto the lines. The large stress level is an important reliability concern for the IC industry. The damascene fabrication methodology changes the magnitude and distribution of stress in the Al interconnect lines. Unpassivated, damascene Al lines have a purely hydrostatic stress. Even though the deposition temperature of the metal and ILD are the same for RIE and damascene. Al lines, the hydrostatic stress of passivated, damascene Al lines (411 MPa) and the maximum shear stress in the lines are sharply reduced. Comparing damascene Al and Cu lines, it is found that the stresses are much smaller in Cu than Al (Hydrostatic stress of 286 MPa), suggesting that stress-induced voiding may be less of a reliability concern for Cu.
A comparative analysis on the bisecting K-means and the PDDP clustering algorithms (2004)

This paper deals with the problem of clustering a data set. In particular, the bisecting divisive partitioning approach is here considered. We focus on two algorithms: the celebrated K-means algorithm, and the recently proposed Principal Direction Di
Superbase-catalysed addition of methanol to propyne and allene: an expedient synthesis of 2-methoxypropene (2006)

In the superbase catalytic systems ButOK/NMP, AmtOCs/NMP and KOH/DMSO, methanol readily adds to propyne and allene at 100–120 °C and atmospheric pressure to afford 2-methoxypropene in 80–97% yield with 75–94% methanol conversion.
Preparation of N-doped TiO2 particles by plasma surface modification (2005)

A cold plasma is useful for surface modification of solid materials. In this work, plasma surface modification is tried to prepare visible-light active TiO 2 particles of which the surface is doped with nitrogen. A film composed of the particles was formed on the surface of a glass substrate by spin-casting of TiO 2 sol and then was sintered at 673 K. The film was treated with argon and nitrogen plasmas, in series. The plasma-treated film revealed visible-light absorption, in addition to ultraviolet-light absorption. Photocatalytic activity of the film was evaluated by using methylene blue and visible-light (wavelength &gt; 420 nm). An increase of the photocatalytic activity in the film will be originated by the formation of Ti–N bonds which bring about the appearance of the visible-light activity. .