gebhart/patrepeval huggingface dataset:
Abstract SY17-03: Tumor-associated antigen MUC1 vaccine for colon cancer prevention (2021)

Abstract For most human cancers, infectious etiology is unknown and preventative vaccines based on viral antigens, such as HPV for cervical cancer, are not a possibility. However, non-viral cancer-associated antigens, self-antigens abnormally expressed on tumors, have been identified as candidates for vaccines. In patients diagnosed with cancer, preexisting immunity to some of these antigens correlates with better disease outcome or reduced risk of recurrence. In transgenic mice or other animal models where they are expressed as self-antigens, immune responses induced to their tumor forms protect from tumor challenge without causing autoimmunity. Therapeutic vaccines that have utilized these antigens have had only marginal efficacy, which extensive research has now attributed to the presence of many immunosuppressive influences in the tumor microenvironment. MUC1 is one such antigen that has been shown effective as a vaccine in preclinical animal models but has had limited immunogenicity and little efficacy as a therapeutic vaccine in numerous clinical trials in many epithelial tumors, including cancer. Hypothesizing that the major difference between the outcome of the vaccine in preclinical models and in clinical trials is likely to be the high level of immune suppression in cancer patients, we began to develop models and MUC1 vaccines for cancer prevention in patients at risk, before immune suppression develops. We determined first that the tumor form of MUC1 was expressed on early premalignant lesions as well and chose premalignant colonic polyps as the first setting for testing the preventative vaccine. Data will be reviewed from a published feasibility study confirming immunogenicity and safety of the MUC1 vaccine in healthy individuals at risk for colon cancer. Data will then be presented from a recently completed unpublished randomized, double blind placebo controlled multi-center prophylactic MUC1 vaccine trial in the same patient population, those with a history of advanced colonic polyps and therefore at increased risk of developing colon cancer. Citation Format: Olivera (Olja) J. Finn. Tumor-associated antigen MUC1 vaccine for colon cancer prevention [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr SY17-03.
Power Noise and Near-Field EMI of High-Current System-in-Package With VR Top and Bottom Placements (2019)

Integrated voltage regulators (IVRs) support an increasing number of voltage domains while enhancing the transient response and enabling fine-grained dynamic voltage frequency scaling. A voltage regulator (VR)-on-package is a promising IVR topology, which supports high-voltage transmission within a printed circuit board and package, leading to lower distribution loss. A power delivery network within a VR-on-package environment is presented in this paper. This paper also presents a study of VR topand bottom-placement topologies within a system-in-package environment in terms of electromagnetic interference (EMI) and power integrity. This comparative analysis targets a specific server package application, and the power integrity evaluation is focused on the power delivery network between the VR and IC. The VR top-placement topology exhibits more than 3× less EMI and 15.3% lower worse case IR drop as compared with the VR bottom-placement topology. The tradeoffs are, however, a greater package power loss and higher package cost due to the larger number of package layers in the VR top-placement topology. The VR top-placement topology exhibits a 52.6% higher power loss through the package than the VR bottom-placement topology.
Gate control of superconducting current: Mechanisms, parameters and technological potential (2023)

In conventional metal-oxide semiconductor (CMOS) electronics, the logic state of a device is set by a gate voltage (VG). The superconducting equivalent of such effect had remained unknown until it was recently shown that a VG can tune the superconducting current (supercurrent) flowing through a nanoconstriction in a superconductor. This gate-controlled supercurrent (GCS) effect can lead to superconducting logics like CMOS logics, but with lower energy dissipation. The physical mechanism underlying the GCS effect, however, remains under debate. In this review article, we illustrate the main mechanisms proposed for the GCS effect, and the material and device parameters that mostly affect it based on the evidence reported. We will come to the conclusion that different mechanisms are at play in the different studies reported so far. We then outline studies that can help answer open questions on the effect and achieve control over it, which is key for applications. We finally give insights into the impact that the GCS effect can have towards high-performance computing with low-energy dissipation and quantum technologies.
Reassessment of Liquid/Solid Equilibrium in Ni-Rich Side of Ni-Nb and Ni-Ti Systems (2010)

The liquidus and solidus for the Ni-rich side of the Ni-Nb and Ni-Ti systems on a region of Ni-Nb and Ni-Ti systems of <10 mass% Nb or Ti were measured in order to establish the phase equilibria between the liquid and fcc phases. The thermodynamic parameters for both systems were reassessed based on the experimental data. The calculated liquidus and solidus agree well with the measured values of Ni-base superalloys as well as the present binary data.
WDR1 expression in the normal and noise-damaged chick vestibule (2008)

Unlike mammals, avian cochlear hair cells can regenerate after acoustic overstimulation. The WDR1 gene is one of the genes suspected to play an important role in this difference. In an earlier study, we found that the WDR1 gene is over-expressed in the chick cochlea after acoustic overstimulation. The aim of this study was to compare the expression of WDR1 before and after acoustic overstimulation in the chick vestibule. Seven-day-old chicks were divided into three groups: normal group, damage group, and regeneration group. The damage and regeneration group was exposed to 120 dB SPL white noise for 5-6 hours. The damage group was euthanized shortly after the impulse, but the regeneration group was allowed to recover for 2 days. The utricle, saccule, and the three ampullae of each semicircular canal were dissected and immunohistochemically stained with anti-WD40 repeat protein 1 antibody. For quantitative analysis, immunoreactive densities were measured and quantitative real-time RT PCR was performed. WD40 repeat protein 1 expression was elevated in all the semicircular canals and utricle, two days after an acoustic overstimulation (P=0.001). WDR1 mRNA expression was 1.34 times higher in the regeneration group compared to the normal group, but it was not statistically significant. Exceptionally, WD40 repeat protein 1 expression did not increase in the saccule of the regeneration group. Elevated WDR1 expression in the avian vestibule may have a role in the hair cell regenerating ability as in the avian cochlea. A similar mechanism of hair cell regeneration may exist in the avian cochlea and vestibule.
Real-time Highly Sensitive Measurement of Myocardial Infarction Biomarkers Using Silicon-based Ellipsometric Biosensors (2019)

$2^{\circ}$ 기울어진 산화막 코팅 실리콘 기판의 바이오칩과 프리즘으로 제작한 바이오센서와 검광자 회전 타원편광계를 이용하여 심근경색 생체표지자인 미오글로빈과 cTnI의 진단 농도를 수백 초 내에 실시간 초고감도로 측정하는데 성공하였다. 러닝 버퍼로는 순수한 phosphate buffered saline (PBS) 또는 PBS에 10% ...
Annexin A8 displays unique phospholipid and F‐actin binding properties (2006)

Annexin A8 is a poorly characterized member of the annexin family of Ca2+-regulated membrane binding proteins. Initially only identified at the cDNA level it had been tentatively linked to acute promyelocytic leukaemia (APL) due to its high and regulated expression in APL-derived cells. Here we identify unique properties of the annexin A8 protein. We show that it binds Ca2+-dependently and with high specificity to phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2) and is also capable of interacting with F-actin. In line with these characteristics annexin A8 is recruited to F-actin-associated PtdIns(4,5)P2-rich membrane domains formed in HeLa cells upon infection with non-invading enteropathogenic Escherichia coli. These properties suggest a role of annexin A8 in the organization of certain actin-associated membrane domains.
Trans-saccadic adaptation of perceived size independent of saccadic adaptation (2020)

Systematic shortening or lengthening of target objects during saccades modifies saccade amplitudes and perceived size of the objects. These two events are concomitant when size change during the saccade occurs asymmetrically, thereby shifting the center of mass of the object. In the present study, we asked whether or not the two are necessarily linked. We tested human participants in symmetrical systematic shortening and lengthening of a vertical bar during a horizontal saccade, aiming to not modify the saccade amplitude. Before and after a phase of trans-saccadic changes of the target bar, participants manually indicated the sizes of various vertically oriented bars by open-loop grip aperture. We evaluated the effect of trans-saccadic changes of bar length on manual perceptual reports and whether this change depended on saccade amplitude. As expected, we did not induce any change in horizontal or vertical components of saccade amplitude, but we found a significant difference in perceived size after the lengthening experiment compared to after the shortening experiment. Moreover, after the lengthening experiment, perceived size differed significantly from pre-lengthening baseline. These findings suggest that a change of size perception can be induced trans-saccadically, and its mechanism does not depend on saccadic amplitude change.
Genomic Effects Associated With Response to Placebo Treatment in a Randomized Trial of Irritable Bowel Syndrome (2022)

<b>Background and Aims:</b> Irritable bowel syndrome (IBS), a functional pain disorder of gut-brain interactions, is characterized by a high placebo response in randomized clinical trials (RCTs). Catechol-O-methyltransferase (<i>COMT</i>) rs4680, which encodes high-activity (val) or low-activity (met) enzyme variants, was previously associated with placebo response to sham-acupuncture in an IBS RCT. Examining <i>COMT</i> effects and identifying novel genomic factors that influence response to placebo pills is critical to identifying underlying mechanisms and predicting and managing placebos in RCTs. <b>Methods:</b> Participants with IBS (<i>N</i> = 188) were randomized to three placebo-related interventions, namely, double-blind placebo (DBP), open-label placebo (OLP), or simply trial enrollment without placebo treatment [no placebo (i.e., no pill) treatment control (NPC)], for 6 weeks. <i>COMT</i> rs4680, gene-set, and genome-wide suggestive (<i>p</i> < 10<sup>-5</sup>) loci effects on irritable bowel symptom severity score (IBS-SSS) across all participants were examined. <b>Results:</b> Participants with IBS homozygous for rs4680 met (met/met) had the greatest improvement across all arms, with significantly greater improvement compared to val/val in DBP (beta (SE), -89.4 (42.3); <i>p</i> = 0.04). Twelve genome-wide suggestive loci formed a gene regulatory network highly connected to <i>EGR1</i>, a transcription factor involved in placebo-related processes of learning, memory, and response to stress and reward. <i>EGR1</i> gene expression in peripheral blood mononuclear cells (PBMC) was significantly reduced at the endpoint across all treatment arms (log fold-change, -0.15; <i>p</i> = 0.02). Gene-set enrichment analysis returned three genome-wide significant ontology terms (GO:0032968, GO:0070934, and GO:0070937) linked to transcription regulation and GO:0003918 associated with DNA topoisomerase regulation. <b>Conclusion:</b> These results suggest common molecular mechanisms in response to varying forms of placebo that may inform personalized IBS treatment and placebo response prediction. <b>Clinical Trial Registration:</b> ClinicalTrials.gov, Identifier: NCT0280224.
APPLICATION OF GENE IN COMBINATION WITH A SCHWANN CELL IMPLANT IN THE TRANSECTED ADULT RAT THORACIC SPINAL CORD- A PRELIMINARY REPORT (2002)

In the Bunge repair strategy, a tube containing a Schwann cell cable bridges the cord lesion. Regenerating axons penetrate the proximal cord-graft interface and grow through the Schwann cell cable but the axons do not grow across distal cord-graft interface and into distal cord stump. Regeneration of axons can be promoted by applying neurotrophic factors in graft. Adding a matrix containing genes encoding for neurotrophic factors in the SC bridge between the proximal and distal cord-graft interfaces may promote axonal regeneration into the graft and the distal cord stump. Methods: There were 22 female fisher rats. One segment of 5-mm spinal cord was removed at T9 level. 6 of them (group1) received Schwann cell grafts positioned between transected stumps to test their efficacy to serve as bridges for axonal regeneration. 16 of them (group 2) received gene-treated Schwann cell grafts. All animals survived 4 weeks. Functional result was assessed by BBB behavior test everyweek after surgery. Fast-Blue injection into SC cable one week before perfusion. Immunocytochemistry to detect labeled neurons in cord, brain stem, and cortex. Toluidine blue stain for myelinated axons. Results: A bridge between the severed stumps had been formed in all animals, as determined by the gross and histological appearance and the ingrowth of propriospinal axons from both stumps. In group 1, near the bridge midpoint there was a mean of 1800 myelinated axons and eight times as many nonmyelinated, ensheathed axons. In group 2, more fibrous tissue surrounding grafted cords were noted. Myelinated axons can hardly find in group 2 animals excepted some unmyelinated axons. Histological examination shows vigorous inflammatory reaction with Macrophage dominant in the bridges. Conclusions: This study demonstrates that Schwann cell grafts serve as bridges that support regrowth of both ascending and descending axons across a gap in the adult rat spinal cord. The ground substance of gene-treated graft induced foreign body reaction that inhibits axon regeneration. Additional intervention will be required to eliminate this adverse reaction of the ground substance of gene-treated SC graft.
Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer (2019)

Tumour necrosis factor (TNF) is a cytokine belonging to a family of trimeric proteins; it has been shown to be a key mediator in autoimmune diseases such as rheumatoid arthritis and Crohn's disease. While TNF is the target of several successful biologic drugs, attempts to design small molecule therapies directed to this cytokine have not led to approved products. Here we report the discovery of potent small molecule inhibitors of TNF that stabilise an asymmetrical form of the soluble TNF trimer, compromising signalling and inhibiting the functions of TNF in vitro and in vivo. This discovery paves the way for a class of small molecule drugs capable of modulating TNF function by stabilising a naturally sampled, receptor-incompetent conformation of TNF. Furthermore, this approach may prove to be a more general mechanism for inhibiting protein-protein interactions.
DAF-16 recruits the CREB-binding protein coactivator complex to the insulin-like growth factor binding protein 1 promoter in HepG2 cells (2000)

Insulin negatively regulates expression of the insulin-like growth factor binding protein 1 (IGFBP-1) gene by means of an insulin-responsive element (IRE) that also contributes to glucocorticoid stimulation of this gene. We find that the Caenorhabditis elegans protein DAF-16 binds the IGFBP-1 small middle dotIRE with specificity similar to that of the forkhead (FKH) factor(s) that act both to enhance glucocorticoid responsiveness and to mediate the negative effect of insulin at this site. In HepG2 cells, DAF-16 and its mammalian homologs, FKHR, FKHRL1, and AFX, activate transcription through the IGFBP-1.IRE; this effect is inhibited by the viral oncoprotein E1A, but not by mutants of E1A that fail to interact with the coactivator p300/CREB-binding protein (CBP). We show that DAF-16 and FKHR can interact with both the KIX and E1A/SRC interaction domains of p300/CBP, as well as the steroid receptor coactivator (SRC). A C-terminal deletion mutant of DAF-16 that is nonfunctional in C. elegans fails to bind the KIX domain of CBP, fails to activate transcription through the IGFBP-1.IRE, and inhibits activation of the IGFBP-1 promoter by glucocorticoids. Thus, the interaction of DAF-16 homologs with the KIX domain of CBP is essential to basal and glucocorticoid-stimulated transactivation. Although AFX interacts with the KIX domain of CBP, it does not interact with SRC and does not respond to glucocorticoids or insulin. Thus, we conclude that DAF-16 and FKHR act as accessory factors to the glucocorticoid response, by recruiting the p300/CBP/SRC coactivator complex to an FKH factor site in the IGFBP-1 promoter, which allows the cell to integrate the effects of glucocorticoids and insulin on genes that carry this site.
Large animal<i>in vivo</i>evaluation of a binary blend polymer scaffold for skeletal tissue-engineering strategies; translational issues (2015)

Binary blend polymers offer the opportunity to combine different desirable properties into a single scaffold, to enhance function within the field of tissue engineering. Previous in vitro and murine in vivo analysis identified a polymer blend of poly(l-lactic acid)-poly(ε-caprolactone) (PLLA:PCL 20:80) to have characteristics desirable for bone regeneration. Polymer scaffolds in combination with marrow-derived skeletal stem cells (SSCs) were implanted into mid-shaft ovine 3.5 cm tibial defects, and indices of bone regeneration were compared to groups implanted with scaffolds alone and with empty defects after 12 weeks, including micro-CT, mechanical testing and histological analysis. The critical nature of the defect was confirmed via all modalities. Both the scaffold and scaffold/SSC groups showed enhanced quantitative bone regeneration; however, this was only found to be significant in the scaffold/SSCs group (p = 0.04) and complete defect bridging was not achieved in any group. The mechanical strength was significantly less than that of contralateral control tibiae (p < 0.01) and would not be appropriate for full functional loading in a clinical setting. This study explored the hypothesis that cell therapy would enhance bone formation in a critical-sized defect compared to scaffold alone, using an external fixation construct, to bridge the scale-up gap between small animal studies and potential clinical translation. The model has proved a successful critical defect and analytical techniques have been found to be both valid and reproducible. Further work is required with both scaffold production techniques and cellular protocols in order to successfully scale-up this stem cell/binary blend polymer scaffold. © 2015 The Authors. Journal of Tissue Engineering and Regenerative Medicine published by John Wiley & Sons, Ltd.
Air Temperature Distribution and the Influence of Sky View Factor in a Green Singapore Estate (2009)

This paper investigates, first, the influence of vegetations to the air temperature distribution and, second, the correlation between air temperature and sky view factor (SVF) to understand whether the trees have adverse impact especially to the nighttime air temperature since trees reduce the SVF values. Air temperature and SVF measurements were conducted in a green Singapore estate, One-North, from November 1, 2007 to March 31, 2008. The field measurement results show that daytime air temperature difference between dense greenery area and less greenery area is 2.4 K and the nighttime air temperature difference is 1.1 K. The temperature maps study provides a clear picture on the air temperature distribution across the One-North estate and concludes that parks or clusters of trees are able to maintain both daytime and nighttime air temperature at a cool level. Statistical analysis was conducted to analyze the correlation between air temperature and SVF. During daytime, there is a significant and good correlation between air temperature and SVF. The higher the SVF, the higher is the air temperature. Trees reduce the sky openness and provide shading to the environment. At nighttime, there is a weak correlation between air temperature and SVF. Thus, there is no adverse impact, i.e., reduction of nighttime net long-wave loss, due to the reduction of SVF by trees.
Intimal pulmonary artery sarcoma presenting as dyspnea: case report (2007)

Pulmonary artery sarcomas are a difficult diagnosis. The diagnosis may remain elusive for some time until the proper imaging techniques are utilized to make a diagnosis. Earlier and accurate diagnosis may lead to earlier interventions and improve survival.
DONOR AND RECIPIENT PRETRANSPLANT CONDITIONING WITH NONLETHAL RADIATION AND ANTILYMPHOCYTE SERUM IMPROVES THE GRAFT SURVIVAL IN A RAT SMALL BOWEL TRANSPLANT MODEL1,2 (2001)

Donor preconditioning with 250 rd and or ALS combined with recipient preconditioning and donor-specific bone marrow infusions prevented GVHD and resulted in a transient mixed chimerism with inhibition of allograft rejection after small bowel transplantation.
Spinel materials for Li-ion batteries: new insights obtained by<i>operando</i>neutron and synchrotron X-ray diffraction (2015)

In the last few decades Li-ion batteries changed the way we store energy, becoming a key element of our everyday life. Their continuous improvement is tightly bound to the understanding of lithium (de)intercalation phenomena in electrode materials. Here we address the use of operando diffraction techniques to understand these mechanisms. We focus on powerful probes such as neutrons and synchrotron X-ray radiation, which have become increasingly familiar to the electrochemical community. After discussing the general benefits (and drawbacks) of these characterization techniques and the work of customization required to adapt standard electrochemical cells to an operando diffraction experiment, we highlight several very recent results. We concentrate on important electrode materials such as the spinels Li1 + xMn2 - xO4 (0 ≤ x ≤ 0.10) and LiNi0.4Mn1.6O4. Thorough investigations led by operando neutron powder diffraction demonstrated that neutrons are highly sensitive to structural parameters that cannot be captured by other means (for example, atomic Debye-Waller factors and lithium site occupancy). Synchrotron radiation X-ray powder diffraction reveals how LiMn2O4 is subject to irreversibility upon the first electrochemical cycle, resulting in severe Bragg peak broadening. Even more interestingly, we show for the first time an ordering scheme of the elusive composition Li0.5Mn2O4, through the coexistence of Mn(3+):Mn(4+) 1:3 cation ordering and lithium/vacancy ordering. More accurately written as Li0.5Mn(3+)0.5Mn(4+)1.5O4, this intermediate phase loses the Fd\overline 3m symmetry, to be correctly described in the P213 space group.