gebhart/patrepeval huggingface dataset:
Abstract 3227: Differential expression of T cell co-inhibitory receptors: KLRG1 alignment with cytotoxicity and adaptive resistance mechanisms (2019)

Abstract Introduction: KLRG1 is a lymphocyte co-inhibitory, or immune checkpoint, receptor expressed predominantly on late-differentiated effector and effector memory CD8+ T and NK cells. Methods: We studied KLRG1 expression in human blood and tumor samples from available genomic datasets. Results: KLRG1 is differentially expressed from CTLA-4 and PD-1, with predominant expression on cytotoxic CD8 T and NK cells over CD4 T cells. Within the CD8+ T cell population, KLRG1 expression, unlike CTLA-4 and PD-1 expression, is linked to greater antigen-driven differentiation states, with increased expression on CD45RO+CCR7- T effector memory (TEM) and CD45RA+CCR7- T effector memory RA (TEMRA) cells compared to CD45RA+CCR7+ naïve T cells (TN) and CD45RO+CCR7+ central memory T cells (TCM). The cytotoxic potential of CD8+ T cells, as assessed by the presence of cytokine and cytotoxic molecules IFNg, TNFa, perforin and granzyme B, is aligned with KLRG1, but not CTLA-4 or PD-1, expression. In single cell RNAseq analyses, KLRG1+ TILS accounted for 16-48% of CD8+ TILS, a frequency similar to that of PD-1+ TILS, in renal cell carcinoma, hepatocellular carcinoma, melanoma, ovarian cancer, HNSCC, and astrocytoma. KLRG1 expression was numerically increased post-treatment in 20/21 (95%) of datasets, statistically significant in 10/21 (48%), in response to a range of treatments including radiotherapy, chemotherapy, endocrine therapy, and immunotherapies (including ipilimumab, nivolumab, and pidilizumab), over periods of time ranging from 1-25 weeks. Conclusions: In human blood and tumor samples, KLRG1 expression is aligned with cytotoxic T and NK cell differentiation, and upregulated in human tumor samples after a variety of therapies, potentially contributing to adaptive resistance. The upregulation of KLRG1 could contribute to limited efficacy and adaptive resistance that develops with current immunotherapies, and suggests KLRG1 blockade may work efficaciously, including as a neo-adjuvant therapy. Citation Format: Steven A. Greenberg, Evan Thompson, Stefano V. Gulla. Differential expression of T cell co-inhibitory receptors: KLRG1 alignment with cytotoxicity and adaptive resistance mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3227.
S0336 Healthcare Provider Perspectives on Lowering Colorectal Cancer Screening Initiation Age to 45 Years (2020)

INTRODUCTION: For most professional organizations in the US, including the US Preventive Services Task Force, age 50 years is the historical threshold for initiating average risk colorectal cancer (CRC) screening. In 2018, in response to increasing CRC incidence and mortality in younger patients, the American Cancer Society issued a qualified recommendation to begin average-risk CRC screening at age 45 years. Provider recommendation is the most consistent factor associated with CRC screening; thus, it is critical to understand clinician perspectives on the appropriate age for initiation. METHODS: We implemented a web survey with an online panel of primary care clinicians (PCCs) and gastroenterologists (GIs) to assess CRC screening knowledge, attitudes, and behaviors. Data were collected from November to December, 2019. Clinicians were asked: “Should the age to begin CRC screening for patients at average risk of developing CRC be lowered from age 50 to age 45?” We evaluated bivariate (Chi-square) and multivariable (logistic regression) associations of clinician- and practice-level factors associated with agreement. RESULTS: Survey responses were received from 814 PCCs and 159 GIs. The survey completion rate was 25.3% for PCCs and 29.6% for GIs. Respondents who indicated specialties other than primary care or gastroenterology (n = 13) and those who reported that they do not recommend CRC screening to their average risk patients or if they reported a CRC mode preference other than gFOBT, FIT, Cologuard, or colonoscopy (n = 42) were excluded from our analyses, resulting in a total analytic sample of n = 938. While 38.1% of PCCs agreed with lowering the screening initiation age to 45 years, 75.5% of GIs agreed (P < .0001). In multivariable analyses, GIs were over 5 times (OR = 5.30; 95% CI 3.54–7.93) more likely than PCCs to endorse lowering the CRC screening initiation age to 45 years. Other factors found to be independently associated with preference for earlier initiation included seeing more than 25 patients per day (vs. fewer) and suburban (vs. urban) location of clinic (Table 1). CONCLUSION: In this national survey, GIs expressed stronger support for initiating average-risk CRC screening at a younger age, compared to PCCs. These data emphasize the need for collaboration between PCCs and GIs to define and discuss the public health implications of earlier-onset CRC screening and ensure that patients receive consistent messaging and optimal evidence-based care.Table 1.: Characteristics of primary care clinicians and gastroenterologists based on agreement to lowering CRC screening start age to 45.
Overcoming Social and Psychological Barriers to Effective On -line Collaboration (2002)

Research suggests that collaboration in an on-line course can enhance learning, reduce feelings of isolation, increase satisfaction with the course, and increase motivation. Unfortunately, creating an environment within which collaboration can occur doesn’t happen automatically. A review of the literature suggests that for on-line collaboration to be most effective, participants must: (1) see the value of expending the (considerable) effort required, (2) be comfortable with and trust the medium, (3) be comfortable with and trust their instructor (or facilitator) and their fellow collaborators, and (4) feel as though they are immersed in a rich, engaging, and rewarding social experience. While many papers suggest that one or more initial face-to-face meetings will expedite trust, familiarity, and a willingness to collaborate, one of the primary reasons why students engage in distance learning is the convenience of anytime, anyplace learning. Thus, face-to-face meetings are not always possible or desirable, leaving us with the need to address these issues in more creative ways. This paper reports on how researchers and practitioners have begun to address the challenges associated with on-line collaboration.
Impact of the Zn diffusion process at the source side of In<inf>x</inf>Ga<inf>1−x</inf>As nTFETs on the analog parameters down to 10 K (2017)

In this work, the impact of the Zn diffusion processes in the source and the amount of Indium for In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1−x</inf> As nTFET was analyzed, focusing on the basic analog parameters. Three different splits were analyzed: In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</inf> As with Spin-on-Glass (SoG) Zn diffusion in the source, In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.7</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.3</inf> As using SoG and In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</inf> As with Gas Phase Zn diffusion in the source. The Ion increase of the Gas Phase device can be related to its higher source/channel junction abruptness that also reduces the tunneling length. The Gas Phase device has presented better subthreshold swing, which increases the transistor efficiency in the weak conduction regime. The Gas Phase device presents the lowest intrinsic voltage gain (A <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</inf> )for high gate voltage (V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GS</inf> ) values due to its significant output conductance (g <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</inf> ) degradation However, the reduction of the temperature affects more g <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</inf> than gm, resulting in an improvement of A <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</inf> by more than 20 dB at 10 K for the Gas Phase device compared to both SoG splits.
Sequence-dependent interaction between cisplatin and histone deacetylase inhibitors in human oral squamous cell carcinoma cells (2006)

Chemotherapeutic treatment with combinations of drugs is front-line therapy for many types of cancer. Combining drugs that target different signaling pathways often lessens adverse side-effects while increasing the efficacy of treatment and reducing patient morbidity. Histone deacetylase (HDAC) inhibitors represent a novel class of anti-neoplastic agents that act by promoting acetylation of core histones, leading in turn to the uncoiling of chromatin and activation of a variety of genes implicated in the regulation of cell survival, proliferation, differentiation, and apoptosis. A defined scheduling protocol is described by which HDAC inhibitors facilitate the cytotoxic effectiveness of cisplatin (CDDP) in the killing of carcinoma cells. An oral squamous cell carcinoma cell line (HSC-3) was treated with sodium butyrate (NaB), suberoylanilide hydroxamic acid (SAHA) or MS-275 on the day of, the day before, or the day after addition of CDDP. The IC50 (48-h assay) value of 3.48 microg/ml CDDP could be lowered to 0.41 microg/ml CDDP when concurrently combined with an HDAC inhibitor (MS-275). The percentage of apoptosis by treatment with CDDP for 24 h, followed by NaB for an additional 24 h without washing was significantly greater than that observed in the reverse order. Depending on the time of addition of HDAC inhibitors, CDDP-treated cells displayed varying degrees of apoptotic responses, indicating the critical nature of timing in the use of HDAC inhibitors. Interestingly, experiments suggested that cells arrested at the G1/S checkpoint by CDDP were more sensitive to subsequent treatment with an HDAC inhibitor. Moreover, these events were associated with an enhancement of reactive oxygen species (ROS) generation and caspase-3 activation by HDAC inhibitors. They raise the possibility that combining these agents may represent a novel anti-neoplastic strategy.
Artificial Molecular Rotary Motors Based on Rotaxanes (2004)

This chapter contains sections titled: “Molecular Machines” — Reality or Just a Fashionable Term? Tracing Back ATP Synthesis in Living Cells Rotaxanes as Artificial Analogs to Molecular Motors? Rotaxane Synthesis via Template Effects How to Achieve Unidirectional Rotation in Artificial Molecular Motors? The Fuel for Driving the Motor: Light, Electrons, and Chemical Energy Conclusions References
In vitro and in vivo antibacterial activities of the fluoroquinolone WIN 49375 (amifloxacin) (1985)

WIN 49375 (amifloxacin) is a synthetic antibacterial agent of the quinolone class. It is similar in chemical structure to pefloxacin but differs by containing a methylamino, rather than an ethyl, substituent at the 1-N position. The activity of WIN 49375 in vitro was comparable to those of norfloxacin and pefloxacin against Enterobacteriaceae and generally greater than those of tobramycin and cefotaxime. WIN 49375 was more active in vitro than carbenicillin and mezlocillin against Pseudomonas aeruginosa isolates and showed moderate activity against Staphylococcus aureus, with MICs of less than or equal to 2 micrograms/ml. The in vitro activity of WIN 49375 was not markedly affected by the presence of human serum, the size of the bacterial inoculum, or changes in pH between 6 and 8. Against systemic, gram-negative bacterial infections in mice, WIN 49375 was generally less active than cefotaxime but more active than gentamicin. WIN 49548, the major piperazinyl-N-desmethyl metabolite of WIN 49375, was aa effective as the parent drug against experimental infections in mice when given parenterally. When administered orally, however, this metabolite was less potent than WIN 49375. WIN 49375 was highly active by the oral route, with 50% effective doses within two- to threefold of those obtained with parenteral medication.
[Removal pathway and influence factors of hydroponic bio-filter method for nitrogen and phosphorus]. (2007)

Study was made on the use of hydroponic bio-filter method (HBFM) for eutrophic surface water. Results show that HBFM can remove 16.8% of TN and 30.8% of TP at the hydraulic loading rate (HLR) of 3.0 m3/(m2 x d). The removal loading rate of TN and TP can accordingly reach 1.0 and 0.1 g/(m2 x d) respectively. The sedimentation of particulate nitrogen and particulate phosphorus plays a major role in nitrogen and phosphorus removal, and its contribution is 62.2% and 75.9% respectively. The optimal HLR of HBFM ranges from 3.0 to 4.0 m3/(m x d). The intension of secateur for Nasturtium officinale has some effect on its uptake rate, thus the length of cut when harvesting should be less than 10 cm. The harvesting frequency of once a month for Nasturtium officinale has no effect on nitrogen and phosphorus removal of HBFM.
Metal ion encapsulation: cobalt cages derived from polyamines, formaldehyde, and nitromethane (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal ion encapsulation: cobalt cages derived from polyamines, formaldehyde, and nitromethaneR. J. Geue, T. W. Hambley, J. M. Harrowfield, A. M. Sargeson, and M. R. SnowCite this: J. Am. Chem. Soc. 1984, 106, 19, 5478–5488Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/ja00331a016https://doi.org/10.1021/ja00331a016research-articleACS PublicationsRequest reuse permissionsArticle Views6590Altmetric-Citations177LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Physiological response of Pichia pastoris GS115 to methanol-induced high level production of the Hepatitis B surface antigen: catabolic adaptation, stress responses, and autophagic processes (2012)

In the methanol fed-batch phase P. pastoris is exposed to dual stress; stress resulting from methanol degradation and stress resulting from the production of the recombinant protein leading to the induction of oxidative stress and unfolded protein response pathways, respectively. Finally, the modest increase of methanol assimilatory enzymes compared to the strong increase of methanol dissimilatory enzymes suggests here a potential to increase methanol incorporation into biomass/product through metabolic enhancement of the methanol assimilatory pathway.
Interferons lambda, new cytokines with antiviral activity (2013)

Interferons (IFNs) are key cytokines in the establishment of a multifaceted antiviral response. Three distinct types of IFNs are now recognized (type I, type II, and type III) based on their receptor usage, structural features and biological activities. Although all IFNs are important mediators of antiviral protection, their roles in antiviral defence vary. Interferon lambda (IFN-λ) is a recently discovered group of small helical cytokines capable of inducing an antiviral response both in vitro as well as in vivo. They were discovered independently in 2003 by the groups of Sheppard and Kotenko. This family consists of three structurally related IFN-λ subtypes called IFN-λ1 (IL-29), IFN-λ2 (IL-28A), and IFN-λ3 (IL-28B). In this study we investigate the antiviral activities of IFN-λ1, λ2, and λ3 on some medically important viruses, influenza viruses, herpes viruses and lymphocytic choriomeningitis virus.
A high-speed morpheme-extraction system using dictionary database (2003)

Presents a high-speed morpheme-extraction system that extracts morphemes from a phoneme string using the characteristics of a dictionary database. To realize this, a dictionary database access method, a tree-structured index and a parallel index-access technique are introduced. The tree-structured index is divided into an upper part and a lower part, and it is structured to execute parallel accesses. The optimum index structure, which can realize the maximum performance/cost ratio of the morpheme-extraction system, is obtained by evaluating the memory contentions and the amount of memory. This system with its parallelized index is expected to perform morpheme extraction as fast as speech input.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
From glow-sticks to sensors: single-electrode electrochemical detection for paper-based devices (2022)

A versatile biosensing platform based on a single electrode electrochemical system, paper-based devices and glow sticks.
EGFR Mutation Analysis of Circulating Tumor DNA Using an Improved PNA-LNA PCR Clamp Method (2016)

Introduction. Rebiopsies have become more crucial in non-small cell lung cancer (NSCLC). Instead of invasive biopsies, development of collecting biological data of the tumor from blood samples is expected. We conducted a prospective study to assess the feasibility of detection of epidermal growth factor receptor (EGFR) mutation in plasma samples. Method. NSCLC patients harboring EGFR activating mutations, who were going to receive EGFR-tyrosine kinase inhibitors (TKIs) as first-line treatment, were enrolled in this study. Plasma EGFR activating mutations and the T790M resistance mutation were analyzed by an improved PNA-LNA PCR clamp method, characterized by a 10-fold or more sensitivity compared with the original methods. Result. Six patients with wild-type EGFR and 24 patients with EGFR mutations were enrolled in this study. Pretreatment plasma samples achieved sensitivity of 79%. The 6 patients with wild-type EGFR were all negative for plasma EGFR mutations. At the time of disease progression, plasma T790M mutation was detected in 8 of 16 cases. Absence of T790M before and during TKI treatment and disappearance of activating mutations during TKI treatment were considered as predictors of EGFR-TKIs efficacy. Conclusion. We were able to detect EGFR mutations in plasma samples by using an improved PNA-LNA PCR clamp method.
Visual revelations: graphical tales of fate and deception from Napoleon Bonaparte to Ross Perot (1998)

Part 1 Graphical failures: how to display data badly graphical mysteries. Part 2 Graphical triumphs: graphical answers to scientific questions three graphic memorials a Nobel graph Todai Moto Kurashi picturing an L.A. bus schedule. Part 3 Graphical forms: humble pie double Y-axis graphs tabular presentation a rose by another name trilinear plots implicit graphs. Part 4 Using graphical methods: measuring graphicacy graphs in the presidential campaign - why weren't they used more broadly? visual aids when comparing an apple to the stars. Part 5 Improving graphical presentations: integrating figures and text elegance, grace, impact, and graphical displays sense-lining making readable overhead displays - finally.
Combining DHTs and SONs for Semantic-Based Service Discovery (2009)

The soaring number of available online services calls for distributed architectures to promote scalability, fault- tolerance and semantics; to provide meaningful descriptions of services; and to support their efficient retrieval. Current approaches exploit either Semantic Overlay Networks (SONs) or Distributed Hash Tables (DHTs) sweetened with some ”semantic sugar.” SONs enable semantic driven query answering but are less scalable than DHTs, which on their turn, feature efficient but semantic-free query answering based on ”exact” match. This paper presents the ERGOT system combining DHTs and SONs to enable distributed and semantic-based service discovery. A preliminary evaluation of the system performance shows the suitability of the approach both in terms of recall and number of messages.
An Efficient and Secure Location-based Alert Protocol using Searchable Encryption and Huffman Codes (2021)

Location data are widely used in mobile apps, ranging from location-based recommendations, to social media and navigation. A specific type of interaction is that of location-based alerts, where mobile users subscribe to a service provider (SP) in order to be notified when a certain event occurs nearby. Consider, for instance, the ongoing COVID-19 pandemic, where contact tracing has been singled out as an effective means to control the virus spread. Users wish to be notified if they came in proximity to an infected individual. However, serious privacy concerns arise if the users share their location history with the SP in plaintext. To address privacy, recent work proposed several protocols that can securely implement location-based alerts. The users upload their encrypted locations to the SP, and the evaluation of location predicates is done directly on ciphertexts. When a certain individual is reported as infected, all matching ciphertexts are found (e.g., according to a predicate such as “10 feet proximity to any of the locations visited by the infected patient in the last week”), and the corresponding users notified. However, there are significant performance issues associated with existing protocols. The underlying searchable encryption primitives required to perform the matching on ciphertexts are expensive, and without a proper encoding of locations and search predicates, the performance can degrade a lot. In this paper, we propose a novel method for variable-length location encoding based on Huffman codes. By controlling the length required to represent encrypted locations and the corresponding matching predicates, we are able to significantly speed up performance. We provide a theoretical analysis of the gain achieved by using Huffman codes, and we show through extensive experiments that the improvement compared with fixed-length encoding methods is substantial. © 2021 Copyright held by the owner/author(s).