gebhart/patrepeval huggingface dataset:
Antiapoptotic Activities of Bcl-2 Correlate with Vascular Maturation and Transcriptional Modulation of Human Endothelial Cells (2008)

Overexpression of a caspase-resistant form of Bcl-2 (D34A) in human umbilical vein endothelial cells (ECs) implanted into immunodeficient mice promotes the maturation of human EC-lined microvessels invested by vascular smooth muscle cells (VSMCs) of mouse origin. In contrast, EC implants not overexpressing Bcl-2 form only simple, uncoated EC tubes. Here the authors compare the phenotypes of vessels formed in vivo and the transcriptomes in vitro of EC expressing different forms of Bcl-2. Wild-type Bcl-2, like the caspase-resistant D34A Bcl-2 mutant, is antiapoptotic in vitro and promotes VSMC recruitment in vivo, whereas a G145E mutant that has diminished antiapoptotic activity in vitro does not promote vessel maturation in vivo. The D34A and wild-type forms of Bcl-2, but not the G145E mutant form of Bcl-2, significantly regulate RNA transcripts previously associated with EC-VSMC interactions and VSMC biology, including matrix Gla protein, insulin-like growth factor-binding protein (IGFBP)-2, matrix metalloproteinase (MMP)-14, ADAM17, stanniocalcin-1, and targets of the nuclear factor (NF)-kappa B, cAMP response element-binding (CREB), and activator protein 1 (AP1) transcription factor families. These effects of Bcl-2 on the transcriptome are detected in ECs cultured as angiogenic three-dimensional (3-D) tubes but are attenuated in ECs cultured as 2-D monolayers. Bcl-2-regulated transcription in ECs may contribute to vascular maturation, and support design of tissue engineering strategies using EC.
Production of biosurfactants by Bacillus licheniformis and Candida albicans for application in microbial enhanced oil recovery (2015)

In this study, the bacterium Bacillus licheniformis DSM = 13 strain ATCC 14580 and the yeast Candida albicans IMRU 3669 were used for biosurfactant production. Surface properties of the produced biosurfactants were confirmed by determining the emulsification power as well as surface tension. The crude biosurfactants have been extracted from supernatant culture growth. FTIR analysis confirmed the chemical structure of the produced biosurfactants. The yields of crude biosurfactants were about 1 and 12 g/l for B. licheniformis and C. albicans respectively. Also, the results revealed that the emulsification power has been increased up to 96% and 65% with kerosene for bacterial and yeast strain respectively. Surface tension decreased from 72 to 36 mN/m after 72 h of incubation with B. licheniformis and 45 mN/m after 4 days of incubation with C. albicans. The potential application of this bacterial species in microbial enhanced oil recovery (MEOR) was investigated. The percent of oil recovery were 16.6 and 8.6 wt% for the bacterial and yeast strains respectively, upon application in sand pack column designed to stimulate an oil recovery.
Fault-Tolerant Computer Architecture Modeling and Analysis. (1989)

Abstract : This document is the final report. It describes a three-year research effort to develop an engineering tool capable of supporting design and analysis of large-scale, parallel, fault-tolerant computer architectures (FTCAs). The tool, a software package called Computer-Aided Performance and Reliability Evaluation System (CAPRES), allows an FTCA designer or FTCA-design evaluator to predict, by analytical means, the performance, reliability, and performability of candidate computer architectures executing candidate workloads, rather than requiring costly simulation or prototype testing for such prediction, as is currently the case. The analytic capability of CAPRES will make its most important contribution early in the system engineering cycle, when many candidate designs may appear feasible and the best is far from clear. Designers using CAPRES will be able to examine in a matter of hours or days alternatives that today take weeks or months to assess using conventional methods. Keywords: Computer architecture; Fault-tolerance computing; Performance; Modeling; Computer programs; Parallel computing; Computer modeling; Computerized simulation. (kt)
Patient-Reported Outcomes After Opioid-Sparing Surgery Compared With Standard of Care (2021)

Despite significant progress, excessive opioid prescribing after surgery is still common. 1 This practice increases patient morbidity and introduces pills into the community. 2,3 Although opioid-sparing postoperative pathways offer a novel approach to mitigate these risks, concerns about inferior pain control and patient satisfaction have hindered their adoption. Therefore, the following study compares patient-reported outcomes (PROs) after common operations between an opioidsparing recovery pathway and standard of care.
Fluorocarbon assisted atomic layer etching of SiO2 using cyclic Ar/C4F8 plasma (2013)

The authors demonstrate atomic layer etching of SiO2 using a steady-state Ar plasma, periodic injection of a defined number of C4F8 molecules, and synchronized plasma-based Ar+ ion bombardment. C4F8 injection enables control of the deposited fluorocarbon (FC) layer thickness in the one to several Ångstrom range and chemical modification of the SiO2 surface. For low energy Ar+ ion bombardment conditions, the physical sputter rate of SiO2 vanishes, whereas SiO2 can be etched when FC reactants are present at the surface. The authors have measured for the first time the temporal variation of the chemically enhanced etch rate of SiO2 for Ar+ ion energies below 30 eV as a function of fluorocarbon surface coverage. This approach enables controlled removal of Ångstrom-thick SiO2 layers. Our results demonstrate that development of atomic layer etching processes even for complex materials is feasible.
Wet Chemical Passivation of YBa2Cu3 O 7 − x (1990)

Wet chemical techniques are described for treatment of surfaces, which result in the formation of native compounds known to have little or no reactivity to water. Suitable native compounds include , , , , , and the oxalates. Formation of surface layers in which these nonreactive native compounds are major constituents is verified with x‐ray photoelectron spectroscopy (XPS) measurements on films treated with dilute solutions of ,, , , or . No significant changes are observed in the XPS spectra when the sulfide, sulfate, or oxalate films are dipped in water, while the iodide and fluoride films show evidence of reaction with water. X‐ray diffraction measurements show that the superconducting phase is absent in the sulfide film, but is unaffected by the oxalate and sulfate treatments.
Controlling Drug Delivery During Mechanical Ventilation: Breath-Enhanced Jet Nebulization (2018)

Background:Nebulized aerosol delivery during mechanical ventilation results in profound unregulated aerosol losses, which are a strong function of duty cycle or I/E ratio, bias flow and humidification. The present study describes a novel nebulizer and ventilator circuit that minimizes these influences by utilizing a design that results in aerosol generation primarily during inspiration (breath enhancement) and minimizes expiratory losses (breath actuation). The circuit facilitates control of supplemental humidification and functions independently of the brand of ventilator. Methods:The novel device may be operated continuously or via a stand-alone breath-actuated circuit. During a treatment, a 3-way valve directs all ventilator flow to the nebulizer resulting in aerosol generation primarily during inspiration. Special connections in the ventilator circuit bypass the effects of supplemental humidification and allow nebulizer removal for servicing without breaking the circuit. This combination results in controlled drug delivery of bronchodilators and other potent drugs over all ventilator settings without any electrical support. The addition of a pressure sensitive breath-actuated electrical circuit further increases efficiency affording the potential to deliver higher doses of less potent drugs such as antibiotics. The nebulizer is powered independently of the ventilator by wall gases at 50 PSIG. Nebulizer flows of 2 L/m in the continuous mode and 3.5 L/m during breath actuation were used. In vitro testing was performed on several commonly used ventilators over a wide range of breathing patterns, duty cycles and ventilator modes. The nebulizer was charged with radiolabeled saline and filled to 3 or 6 mL. Inhaled mass (IM) and mass balance were measured. Results:IM (% neb charge) mean ± SE, breath-enhanced 11.4 ± 0.9; breath-enhanced and breath actuated 27.2 ± 0.8. Conclusions:During jet nebulization, breath enhancement overcomes much of the variability in aerosol delivery introduced by the ventilator circuit providing a predictable delivered dose to the patient at any ventilator setting. The addition of breath actuation further enhances aerosol delivery for specialized drugs requiring high doses. The use of wall gases and stand-alone breath actuation standardizes conditions driving the nebulizer independent of ventilator design. Circuit design eliminates variation in humidification effects and allows nebulizer servicing without circuit interruption.
An In Vivo Mouse Model of Human Skin Substitute Containing Spontaneously Sorted Melanocytes Demonstrates Physiological Changes after UVB Irradiation (2005)

Human skin substitutes (HSS) have been developed for repairing burns and other acute or chronic wounds. But although the clinical utility of HSS is well known, scant attention has been paid to their cosmetic properties, especially with regard to color compatibility with the patient's complexion. In this study, we generated an HSS from mixed cell slurries containing keratinocytes and fibroblasts with and without melanocytes on the back of severe combined immunodeficient mice by means of a spontaneous cell-sorting technique. At 16 wk after grafting, Caucasian donor-derived HSS with melanocytes were macroscopically clearly darker than those without melanocytes, and a more darkly pigmented HSS was produced when cells from donors of African descent were seeded. Immunohistochemistry of c-kit, S-100, and HMB45, as well as Fontana-Masson staining and transmission electron microscopy (TEM) demonstrated that melanocytes spontaneously localized to the basal layer. Melanosome transfer to keratinocytes was correctly reorganized, and melanin was evenly dispersed in the basal and suprabasal layers. Colorimetric analysis showed a significantly lower L-value by day 14 following irradiation with 120 mJ per cm2 ultraviolet-B (UVB) (p<0.01), whereas epidermal thickness increased by 50% 1 d after exposure (p<0.01), indicating a normal physiological response to UVB irradiation. These findings suggest that HSS with spontaneously sorted melanocytes offer a means of treating both the structural and cosmetic aspects of skin conditions and trauma, such as pigmentary disorders and skin wounds, by allowing manipulation of the color and population of donor melanocytes.
Advanced LSI-based amperometric sensor array with light-shielding structure for effective removal of photocurrent and mode selectable function for individual operation of 400 electrodes (2014)

We have developed a large-scale integrated (LSI) complementary metal-oxide semiconductor (CMOS)-based amperometric sensor array system called "Bio-LSI" as a platform for electrochemical bio-imaging and multi-point biosensing with 400 measurement points. In this study, we newly developed a Bio-LSI chip with a light-shield structure and a mode-selectable function with the aim of extending the application range of Bio-LSI. The light shield created by the top metal layer of the LSI chip significantly reduces the noise generated by the photocurrent, whose value is less than 1% of the previous Bio-LSI without the light shield. The mode-selectable function enables the individual operation of 400 electrodes in off, electrometer, V1, and V2 mode. The off-mode cuts the electrode from the electric circuit. The electrometer-mode reads out the electrode potential. The V1-mode and the V2-mode set the selected sensor electrode at two different independent voltages and read out the current. We demonstrated the usefulness of the mode-selectable function. First, we displayed a dot picture based on the redox reactions of 2.0 mM ferrocenemethanol at 400 electrodes by applying two different independent voltages using the V1 and V2 modes. Second, we carried out a simultaneous detection of O2 and H2O2 using the V1 and V2 modes. Third, we used the off and V1 modes for the modification of the osmium-polyvinylpyridine gel polymer containing horseradish peroxidase (Os-HRP) at the selected electrodes, which act as sensors for H2O2. These results confirm that the advanced version of Bio-LSI is a promising tool that can be applied to a wide range of analytical fields.
Dentistry Stereoviews Revisited: Part 1-Comic/Satirical Cards. (2019)

Christen and Christen introduced stereoviews related to dentistry to <i>Journal of the History of Dentistry</i> readers with the Herman Knutzen comic series of 1906.<sup>1, 2</sup> In that colorful six card set, Dr. Pullemeasy struggles ferociously with what appears to be a mandibular molar extraction using ice tongs. Post-surgically, the smiling sneering patient heads for the door, thumbing his nose, with the final suggestion that "Now the tooth is out let the dentist whistle for his pay."<sup>1</sup>.
CVD SiNx Anti-reflective Coating for Sub-OSpm Lithography (1995)

This paper reports the investigation of low pressure chemical vapor deposition of SiN, film for bottom antireflective coating (BARC) application in 0.35pm lithography and below. The SiNx material was successfully designed to provide excellent anti-reflective layer which meets various advanced device integration requirements. This BARC process has been found to be manufacturable for deep-UV and I-line lithography.
Reduced-reference image quality assessment using distributed source coding (2008)

This paper presents a reduced-reference image quality assessment scheme using distributed source coding for remotely monitoring image quality. In our scheme, an image server extracts a feature vector from the original image and transmits its Slepian-Wolf syndrome using an LDPC encoder. With the rate of the Slepian-Wolf bitstream chosen according to a predetermined admissible image quality, the receiver can reconstruct the feature vector using its received image, as side information, as long as the quality is higher than the admissible quality. Thus the receiver can determine the received image quality using the reconstructed feature vector. Simulation results show that distributed source coding can reduce the bit-rate of the feature vector by 50% and achieve better compression performance than conventional source coding.
Genetically distinct cell populations in naturally occurring bone marrow-chimeric primates express similar MHC class I gene products. (1990)

The cotton-top tamarin (Saguinus oedipus) is a naturally occurring "A" + "B"----"A" bone marrow-chimeric species. These primates usually are born as dizygotic twins and, due to placental vascular anastomoses, develop sharing each others' bone marrow elements. Strikingly, almost 50% of the PBL of a member of a twin pair are derived from the hematopoietic stem cells of its cotwin. To clarify the mechanisms underlying the maintenance of tolerance in these stable chimeras, MHC gene products have been biochemically characterized in cloned, genetically distinct, male and female lymphocytes from two male/female cotton-top tamarin twin pairs. Extensive MHC class II sharing between the genetically distinct cell populations was not seen in the two twin pairs. This was consistent with the MHC class II polymorphism seen in the species. However, the MHC class I gene products expressed by one member of a twin pair were almost identical to those expressed by its cotwin. A human minisatellite probe demonstrated restriction fragment length polymorphism in DNA from these animals, indicating extensive polymorphism. Thus, MHC class I sharing did not occur due to inbreeding in these animals. Additionally, another bone marrow-chimeric primate species, the common marmoset (Callithrix jacchus), expresses MHC class I molecules with low levels of variation. These studies suggest that the stable chimerism of bone marrow-chimeric primates may be facilitated by MHC class I similarity between the genetically distinct bone marrow derived-cell populations in their circulation.
Quantitative analysis of ligand effects. Part 3. Separation of phosphorus(III) ligands into pure .sigma.-donors and .sigma.-donor/.pi.-acceptors. Comparison of basicity and .sigma.-donicity (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitative analysis of ligand effects. Part 3. Separation of phosphorus(III) ligands into pure .sigma.-donors and .sigma.-donor/.pi.-acceptors. Comparison of basicity and .sigma.-donicityM. Matiur Rahman, Hong Ye Liu, Klaas Eriks, Alfred Prock, and Warren P. GieringCite this: Organometallics 1989, 8, 1, 1–7Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/om00103a001https://doi.org/10.1021/om00103a001research-articleACS PublicationsRequest reuse permissionsArticle Views1819Altmetric-Citations249LEARN 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
Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR (2022)

ABSTRACT Among the major classes of RNAs in the cell, tRNAs remain the most difficult to characterize via deep sequencing approaches, as tRNA secondary structure and nucleotide modifications can both interfere with cDNA synthesis by commonly-used reverse transcriptases (RTs). Here, we benchmark a recently-developed RNA cloning protocol, termed Ordered Two-Template Relay (OTTR), to characterize intact tRNAs and tRNA fragments in budding yeast and in mouse tissues. We find that OTTR robustly captures full-length tRNAs in budding yeast and in mouse testis, with relatively low levels of premature termination at known barriers – 1-methylguanine, N2,N2-dimethylguanine, and 1-methyladenine – to typical reverse transcriptases. Moreover, these and several other nucleotide modifications leave misincorporation signatures in OTTR datasets which enables their detection without any additional protocol steps. Turning to analysis of small RNAs such as tRNA cleavage products, we compare OTTR with several standard small RNA-Seq protocols, finding that OTTR provides the most accurate picture of tRNA fragment levels by comparison to “ground truth” Northern blots. Applying this protocol to mature mouse spermatozoa, our data dramatically alter our understanding of the small RNA cargo of mature mammalian sperm, revealing a far more complex population of tRFs – including both 5’ and 3’ tRNA halves derived from the majority of tRNAs – than previously appreciated. Taken together, our data confirm the superior performance of OTTR to commercial protocols in analysis of tRNA fragments, and force a reappraisal of potential epigenetic functions of the sperm small RNA payload.
Studying fluorous interactions in a series of coordination compounds derived from mono-pyridyl ligands equipped with hydrogen bonding functionality: exploiting anion⋯πF interaction in separating ClO4− anion from a competing mixture of anions (2013)

A series of coordination compounds (both coordination complexes (CCs) and coordination polymers (CPs)) viz. [Cu(L1)4·(SO4)·(DMSO)]CC1, [(H2O)2(DMSO)Cd(L1)2(μ2SO4)(Cd(L1)2·(SO4)·(DMSO)·(H2O)] CC2, [Cu(L2)2(H2O)·(Cl)2] CC3, [Cu(L2)2(μ-SO4)(H2O)]∝ CP1, [{Cu(L2)4(μ-SiF6)}·3H2O]∝ CP2, [{Cu(L3)4(ClO4)}·ClO4·H2O]·CC4, [{Cu(L3)4(H2O)}·H2O·2BF4] CC5, [{(Cl)Cu(L3)4(μ-Cl)Cu(L3)4}·Cl·H2O] CC6, [{Cu2(L3)4(μ-Cl)2·(Cl)2}·H2O] CC7, [Cu(L3)2(Cl)2] CC8, and [{Cu(L4)4·(H2O)2}·SO4·5H2O] CC9 derived from ligands equipped with pyridyl and pentafluorophenyl/phenyl moieties along with hydrogen bonding backbone (amide/urea) with CuII/CdII metal centers have been synthesized and characterized by single crystal X-ray diffraction (SXRD). Their various fluorous interactions along with hydrogen bonding have been investigated. The results show that almost all the coordination compounds except CC9 studied herein display various fluorous interactions; in one such example i.e. in CC4, anion–πF along with other supramolecular interactions (F⋯F, C–H⋯F) shapes the supramolecular assembly, which is exploited to separate environmentally relevant perchlorate anion from a competing mixture of anions viz. SO42−, NO3−, ClO4−, BF4−, Cl− by following in situ synthesis of the corresponding coordination compound.
Cell Mitosis During Skin Wound Healing (1964)

It has been well documented that an open (incised) skin wound through the epidermis and into the underlying dermis, results in a rapid, within 24 hours, and abnormal rise in the epidermal mitotic rate. The mitotic rate may be more than ten times the normal maximum, and is highest among those cells closest to the wound edge and lowest, near the normal rate, about 1 mm. from the wound edge. The decreasing mitotic rate within 1 mm. of the wound edge holds quite constant regardless of the size of the open wound. The theoretical explanation of this situation is presented by Bullough and Laurence (1 and 2) in the following three versions: 1. Following the theory that the epidermis is normally deprived of nutrients, it could be proposed that, since there is a marked hyperaemia around the edges of the wound, the increased mitotic activity may be due simply to a greatly increased supply of nutrients. 2. The high mitotic rate could theoretically be due to the stimulating influence of a "wound hormone" secreted from the wound itself. This has been the commonly accepted theory for nearly half of a century. However, the "wound hormone" theory was fully reviewed by Abercrombie (3), who concluded that in spite of many claims, no hormonal substance with mitogenic activity has been extracted from wound tissue, and the possibility must now be considered that no such substance exists. 3. The situation could be explained on the theory that the epidermis normally contains some substance which inhibits mitotic activity, and that the concentration of this substance is reduced in the immediate vicinity adjacent to the wound. This alternative is presently favored by most researchers in wound healing. The work of this author gives evidence that the zone of the highest mitotic rate in wounds caused by dry ice burns is not immediately adjacent to the wound periphery, as is the acknowledged in the instance of open (incised) wounds.