gebhart/patrepeval huggingface dataset:
Data from Pharmacokinetically Stabilized Cystine Knot Peptides That Bind Alpha-v-Beta-6 Integrin with Single-Digit Nanomolar Affinities for Detection of Pancreatic Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Detection of pancreatic cancer remains a high priority and effective diagnostic tools are needed for clinical applications. Many cancer cells overexpress integrin α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;, a cell surface receptor being evaluated as a novel clinical biomarker.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; To validate this molecular target, several highly stable cystine knot peptides were engineered by directed evolution to bind specifically and with high affinity (3–6 nmol/L) to integrin α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;. The binders do not cross-react with related integrin α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;5&lt;/sub&gt;, integrin α&lt;sub&gt;5&lt;/sub&gt;β&lt;sub&gt;1&lt;/sub&gt;, or tumor-angiogenesis–associated integrin, α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;3&lt;/sub&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Positron emission tomography showed that these disulfide-stabilized peptides rapidly accumulate at tumors expressing integrin α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;. Clinically relevant tumor-to-muscle ratios of 7.7 ± 2.4 to 11.3 ± 3.0 were achieved within 1 hour after radiotracer injection. Minimization of off-target dosing was achieved by reformatting α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;-binding activities across various natural and pharmacokinetically stabilized cystine knot scaffolds with different amino acid content. We show that the primary sequence of a peptide scaffold directs its pharmacokinetics. Scaffolds with high arginine or glutamic acid content suffered high renal retention of more than 75% injected dose per gram (%ID/g). Substitution of these amino acids with renally cleared amino acids, notably serine, led to significant decreases in renal accumulation of less than 20%ID/g 1 hour postinjection (&lt;i&gt;P&lt;/i&gt; &lt; 0.05, &lt;i&gt;n&lt;/i&gt; = 3).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We have engineered highly stable cystine knot peptides with potent and specific integrin α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;-binding activities for cancer detection. Pharmacokinetic engineering of scaffold primary sequence led to significant decreases in off-target radiotracer accumulation. Optimization of binding affinity, specificity, stability, and pharmacokinetics will facilitate translation of cystine knots for cancer molecular imaging. &lt;i&gt;Clin Cancer Res; 18(3); 839–49. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
56 Gb/s DMT Transmission with VCSELs in 1.5 um Wavelength Range over up to 12 km for DWDM Intra-Data Center Connects (2020)

We demonstrate up to 12 km, 56 Gb/s DMT transmission using high-speed VCSELs in the 1.5 um wavelength range for future 400Gb/s intra-data center connects, enabled by vestigial sideband filtering of the transmit signal.
Obstructive Sleep Apnea during REM Sleep and Cardiovascular Disease (2017)

Severe OSA that occurs primarily during REM sleep is associated with higher incidence of a composite cardiovascular endpoint, but in only those with prevalent cardiovascular disease.
Ribonucleic Acud Polymerase in Virions of Newcastle Disease Virus: Comparison with the Vesicular Stomatitis Virus Polymerase (1971)

The virions of Newcastle disease virus (NDV) contained an enzyme that catalyzed the incorporation of ribonucleotides into ribonucleic acid (RNA). Optimal conditions for this polymerase activity were identical to the conditions for the vesicular stomatitis virus (VSV) polymerase, and both enzymes were active for longer times at 32 C than at 37 C. However, the specific activity of the NDV polymerase was less than 3% that of the VSV polymerase. Product RNA species from the NDV and VSV polymerase reactions annealed specifically to the homologous virion RNA species. Transcriptive intermediates containing product RNA attached to the respective virion RNA could be identified in both systems.
Performance analysis of transparent BIPV/T double skin façades integrated with the decision-making algorithm for mixed-mode building ventilation (2023)

ABSTRACTThis study addresses building performance profiles of building-integrated photovoltaic/thermal double-skin façades (BIPV/T-DSF) integrated with the decision-making for the opening control algorithm in the mixed-mode building ventilation system. Three cases were generated and simulated in this study. The integrated case (a focused case) indicated its potential in comparison with two other fixed single-mode ventilated BIPV/T-DSF cases (non-ventilated cavity and cavity ventilated BIPV/T-DSF cases). The mixed-mode building ventilation algorithm was logically generated and implemented in the integrated case to maximize passive heating and cooling while reducing energy consumption, increasing the indoor thermal comfort level, and preventing the overheating of BIPV. The temperatures of spaces used as major criteria in the developed algorithm were identified through optimization analysis. Three cities were chosen to represent three different climates: hot summer continental and cold winter climate (Daejeon, South Korea), tropical savanna (Bangkok, Thailand), and continental subarctic (Tayshet, Russia). Multi-criteria simulation results showed that implementing the logically created mixed-mode building ventilation algorithm in a transparent BIPV/T-DSF has outstanding potential to improve thermal comfort, especially during moderate weather, and somewhat reduces energy consumption compared to the two other studied cases.KEYWORDS: Building-integrated photovoltaic/thermal (BIPV/T) systemdouble skin façades (DSF)mixed mode ventilationbuilding energy savingdecision-makingsensitivity analysis Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by National Research Foundation of Korea [2022R1A2C2010985].
Volume holographic grating for wavelength multiplexed field-of-view expansion (2022)

We propose and demonstrate a Field of View (FOV) expander, realized by wavelength-division multiplexing (WDM) by using volume holographic gratings (VHG). This holographic based FOV expander is low cost and easy to manufacture, which we demonstrate through our updated in-plane writing setup. We present our experimental results of diffraction efficiency measurements and image analysis which show high SNR and angular resolution. This holographic based FOV expander based on VHGs have potentials and can be implemented into AR/VR systems.
Electrical Readout of Carrier Dynamics in Micro-Scale Infrared Materials (2018)

We present a technique, Micro-Scale Microwave Resonator Time Response (μ-MRTR), capable of measuring photo-excited carrier lifetimes in micro-scale material volumes using a resonant microwave circuit with direct electrical readout. We demonstrate a ~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> improvement in sensitivity when compared to traditional lifetime measurement techniques.
Database Transaction Management for High-Availability Cluster System (2006)

We propose a database transaction management framework that enables a database replication function to be added to existing cluster systems. This framework is generally applicable to various database products merely by replacing the database connection API library. In this framework, the enhanced database connection API library duplicates the transactions issued by clustered applications and issues them to the primary and backup databases while controlling the issue order for consistency between the two databases. We implemented the proposed framework on a database connection API library for Java and confirmed that the overhead caused by duplication and order control was smaller than the existing replication method's overhead
Supplementary Data from Selective Killing of SMARCA2- and SMARCA4-deficient Small Cell Carcinoma of the Ovary, Hypercalcemic Type Cells by Inhibition of EZH2: <i>In Vitro</i> and <i>In Vivo</i> Preclinical Models (2023)

&lt;p&gt;PDF File -1 MB, Supplemental data is to further support the statements made it the main text. Captions: Supplemental Table 1: Cell Lines used in the CRISPR pooled screen. Supplemental Table 2: Table of ovarian lines screened for tazemetostat sensitivity along with mutational and protein status for SMARCA2, SMARCA4, and ARID1A. Supplemental Table 3: p-values of COV434 SCCOHT cell line treated with tazemetostat. Supplemental Table 4: p-values of JHOC-5 clear cell ovarian cell line treated with tazemetostat. Supplemental Table 5: p-values of cell cycle analysis after tazemetostat treatment. Supplemental Table 6: p-values of apoptosis analysis after tazemetostat treatment. Supplemental Table 7: LogP scores for SWI/SNF components in ovarian lines +/- tazemetostat treatment. Supplemental Figure 1: Baseline measurement of histone 3 lysine 27 trimethyl mark and EZH2. Supplemental Figure 2a: Growth curves of SCCOHT and ovarian cancer cell lines treated with tazemetostat. Supplemental Figure 2b: Growth curves of SCCOHT and ovarian cancer cell lines treated with EPZ-007210. Supplemental Figure 3: Reduction in H3K27me3 mark after treatment. Supplemental Figure 4a: Sensitivity to PLK1 knockout as pan-essential in CRISPR pooled screen. Supplemental Figure 4b: Control sgRNAs from CRISPR pooled screen. Supplemental Figure 5: TOV112D xenograft tumor growth inhibition, tumor volume, and methyl mark. Supplemental Figure 6: body weights of mice treated with tazemetostat. Supplemental Figure 7: measured blood plasma levels of tazemetostat from xenograft mice.&lt;/p&gt;
Modular Opto-Mechanical Design of Free-Space Optical Interconnect System for Massively Parallel Processing (1997)

Free-space optical interconnections can provide parallel access for many communication patterns with a large bandwidth[1, 2]. The challenge in the realization of such systems relies in finding good solution for the alignment and packaging of the electro-optical components. We present a new modular building block that will address these challenges in a free-space optical network for massively parallel processing (MPP). Our component and system ideas offer a simple method to fabricate and build the optical network assuring reliable and convenient alignment and packaging. We use micro-lens arrays which are pre-aligned and packaged as modular building blocks to relay optical beams from one module to the next. We can apply our modular building block ideas to our previous system of a 64-channel free-space optical interconnection[1] and its wavelength division multiplexing (WDM) extensions[3] to realize a more reliable and easier to build system. In the current network architecture, as well as in the previous ones, we use a nonblocking and reconfigurable interconnection cached network (ICN)[4].
High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds (2023)

Entamoeba histolytica is a disease-causing parasitic amoeba which affects an estimated 50 million people worldwide, particularly in socioeconomically vulnerable populations experiencing water sanitation issues. Infection with E. histolytica is referred to as amoebiasis, and can cause symptoms such as colitis, dysentery, and even death in extreme cases. Drugs exist that are capable of killing this parasite, but they are hampered by downsides such as significant adverse effects at therapeutic concentrations, issues with patient compliance, the need for additional drugs to kill the transmissible cyst stage, and potential development of resistance. Past screens of small and medium sized chemical libraries have yielded anti-amoebic candidates, thus rendering high-throughput screening a promising direction for new drug discovery in this area. In this study, we screened a curated 81,664 compound library from Janssen pharmaceuticals against E. histolytica trophozoites in vitro, and from it identified a highly potent new inhibitor compound. The best compound in this series, JNJ001, showed excellent inhibition activity against E. histolytica trophozoites with EC50 values at 0.29 μM, which is better than the current approved treatment, metronidazole. Further experimentation confirmed the activity of this compound, as well as that of several structurally related compounds, originating from both the Janssen Jump-stARter library, and from chemical vendors, thus highlighting a new structure-activity relationship (SAR). In addition, we confirmed that the compound inhibited E. histolytica survival as rapidly as the current standard of care and inhibited transmissible cysts of the related model organism Entamoeba invadens. Together these results constitute the discovery of a novel class of chemicals with favorable in vitro pharmacological properties. The discovery may lead to an improved therapy against this parasite and in all of its life stages.
Effects of Alkyl-Chain Length of Alkylphosphonic Acids on Thermochromic Behavior of Fluoran Dye. (1995)

フルオラン化合物(FD:2'-(o一クロロアニリノ)-6'-ジブチルアミノスピロ[イソベソゾフラン-1(3H),9'-[9H]キサソテン]-3-オン)のサーモクロミズムに対するアルキルポスホン酸(Pn;nは炭素数)のアルキル鎖長の効果を調べた.P14～22とFDの混合膜は,加熱溶融状態からの徐冷では消色するが,急冷では発色した固体膜となった.これを昇温すると溶融発色温度より約20℃ 低い温度で消色した.アルキル鎖が長いほど発色は安定で,消色温度は高くなり消色性も向上した.一方,P10,P12では急冷しても安定な発色膜は得られず,またP4はタール状の発色膜となるが,昇温しても消色しなかった.X線回折と示差走査熱量測定(DSC)の結果から,Pn/FDの発色固体膜は,アルキル鎖が長いほど密に凝集したラメラ構造を形成しており,昇温によりこの構造が崩れるとホスホン酸が単独の結晶を形成して分離し,消色することがわかった.これらの結果から,長鎖アルキル基の凝集力は,両者が共同した“超分子構造”の形成による発色の安定化と,ホスホン酸の結晶化による消色の両方に有効に作用し,サーモクロミズム特性を与えることが明らかになった.
L-Vinylglycine from L-Homoserine. (1988)

Abstract A simple and practical synthesis of L-vinylglycine starting from L-homoserine is described.
Role of SIRT1-mediated mitochondrial and Akt pathways in glioblastoma cell death induced by Cotinus coggygria flavonoid nanoliposomes (2015)

Flavonoids, the major polyphenol components in Cotinus coggygria (CC), have been found to show an anticancer effect in our previous study; however, the exact mechanisms of inducing human glioblastoma (GBM) cell death remain to be resolved. In this study, a novel polyvinylpyrrolidone K-30/sodium dodecyl sulfate and polyethyleneglycol-coated liposome loaded with CC flavonoids (CCFs) was developed to enhance solubility and the antibrain tumor effect, and the molecular mechanism regarding how CCF nanoliposomes (CCF-NLs) induce apoptotic cell death in vitro was investigated. DBTRG-05MG GBM cell lines treated with CCF-NLs showed potential antiproliferative effects. Regarding the underlying mechanisms of inducing apoptosis in DBTRG-05MG GBM cells, CCF-NLs were shown to downregulate the expression of antiapoptotic B-cell lymphoma/leukemia 2 (Bcl-2), an apoptosis-related protein family member, but the expression of proapoptotic Bcl-2-associated X protein was enhanced compared with that in controls. CCF-NLs also inhibited the activity of caspase-3 and -9, which is the initiator caspase of the extrinsic and intrinsic apoptotic pathways. Blockade of caspase activation consistently induced apoptosis and inhibited growth in CCF-NL-treated DBTRG-05MG cells. This study further investigated the role of the Akt pathway in the apoptotic cell death by CCF-NLs, showing that CCF-NLs deactivated Akt. Specifically, CCF-NLs downregulated the expression of p-Akt and SIRT1 as well as the level of phosphorylated p53. Together, these results indicated SIRT1/p53-mediated cell death was induced by CCF-NLs, but not by extracellular signal-regulated kinase, in DBTRG-05MG cells. Overall, this study suggested caspase-dependent activation of both the intrinsic and extrinsic signaling pathways, probably through blockade of the SIRT1/p53-mediated mitochondrial and Akt pathways to exert the proapoptotic effect of CCF-NLs in DBTRG-05MG GBM cells.
RUGRAT: Evaluating program analysis and testing tools and compilers with large generated random benchmark applications (2014)

Benchmarks are heavily used in different areas of computer science to evaluate algorithms and tools. In program analysis and testing, open-source and commercial programs are routinely used as benchmarks to evaluate different aspects of algorithms and tools. Unfortunately, many of these programs are written by programmers who introduce different biases, not to mention that it is very difficult to find programs that can serve as benchmarks with high reproducibility of results. We propose a novel approach for generating random benchmarks for evaluating program analysis and testing tools and compilers. Our approach uses stochastic parse trees, where language grammar production rules are assigned probabilities that specify the frequencies with which instantiations of these rules will appear in the generated programs. We implemented our tool for Java and applied it to generate a set of large benchmark programs of up to 5M lines of code each with which we evaluated different program analysis and testing tools and compilers. The generated benchmarks let us independently rediscover several issues in the evaluated tools. Copyright © 2014 John Wiley & Sons, Ltd.
A Sub-nW, 8T Current Reference Consuming Constant Power w.r.t Process & Temperature (2020)

The paper presents an eight transistor (8T) pico- watt current reference with a novel method of rectifying the problem of exponential power increase w.r.t temperature in traditional sub-nW references. The proposed current reference is obtained by modifying the traditional beta-multiplier architecture to scale- down the power consumption without sacrificing area. The constancy of power consumption w.r.t temperature is achieved by exploiting the voltage-current characteristics of a leakage transistor in the modified architecture. The proposed current reference, implemented in UMC 55nm technology, occupies an area of 0.00035mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . It is designed for a current of 60pA and achieves an accuracy of 19 ppm/°C over a wide temperature range of -55°C to 125°C. The reported line sensitivity for the current reference is 0.07%/V in the supply range of 1.2V - 4V. Post-trim results show a constant power consumption of 144pW w.r.t temperature and process variations @1.2V supply.
Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii in the Intensive Care Unit of Uruguay's University Hospital Identifies the First rmtC Gene in the Species (2018)

Carbapenem-resistant Acinetobacter baumannii (CRAB) infections are an increasing concern in intensive care units (ICUs) worldwide. The combination of carbapenemases and 16S rRNA-methyltransferases (16S-RMTases) further reduces the therapeutic options. OXA-carbapenemase/A. baumannii clone tandems in Latin America have already been described; however, no information exists in this region regarding the occurrence of 16S-RMTases in this microorganism. In addition, the epidemiology of A. baumannii in ICUs and its associated resistance profiles are poorly understood. Our objectives were as follows: to study the clonal relationship and antibiotic resistance profiles of clinical and digestive colonizing A. baumannii isolates in an ICU, to characterize the circulating carbapenemases, and to detect 16S-RMTases. Patients admitted between August 2010 and July 2011 with a clinically predicted hospital stay > 48 hr were included. Pharyngeal and rectal swabs were obtained during the first fortnight after hospitalization. Resistance profiles were determined with MicroScan<sup>®</sup> and VITEK2 system. Carbapenemases and 16S-RMTases were identified by PCR and sequencing, and clonality was assessed by pulsed-field gel electrophoresis and multilocus sequence typing. Sixty-nine patients were studied and 63 were diagnosed with bacterial infections. Among these, 29 were CRAB isolates; 49 A. baumannii were isolated as digestive colonizers. These 78 isolates were clustered in 7 pulsetypes, mostly belonging to ST79. The only carbapenemase genes detected were bla<sub>OXA-51</sub> (n = 78), bla<sub>OXA-23</sub> (n = 62), and bla<sub>OXA-58</sub> (n = 3). Interestingly, two clinical isolates harbored the rmtC 16S-RMTase gene. To the best of our knowledge, this is the first description of the presence of rmtC in A. baumannii.
IL-2 REGULATES FLIP EXPRESSION IN HUMAN CD4+ LYMPHOCYTES (1999)

262 FLIP is a molecule which inhibits the Fas death pathway by blocking the ability of Caspace 8 to bind to the death complex and initiate Fas killing. Previous studies demonstrate that FLIP is down regulated by IL-2 in murine CD4+ lymphocytes allowing Fas mediated killing through activation induced cell death. The regulation of the Fas pathway is crucial for the development tolerance, where Fas mediated cell death is responsible for peripheral tolerance in lymphocytes. It is therefore important for the development of strategies aimed at tolerance induction to investigate whether IL-2 downregulates FLIP in human lymphocytes. In order to study FLIP expression and regulation, peripheral blood leukocytes were purified from leukopaks. CD4+ lymphocytes were purified from the leukocytes by Dynal beads. The beads were then removed using "detatchabead". 1 ×106 cells were activated by PHA and anti-CD28 and then cultured in C10 media with or without the addition of high doses (100 units) of IL-2. Cells were assayed for apoptosis induced by anti-Fas antibody CH11 at various time points. Apoptosis was assessed by Propidium Iodide staining. 24 hours after the addition of the anti-Fas antibody lymphocytes were harvested washed and fixed in 70% ethanol. The following day the lymphocytes were stained with Propidium Iodide and analyzed by flow cytometry using a B-D FACSscan. CD4+ lymphocytes were resistant to Fas mediated apoptosis. By Day 6 lymphocytes in the presence of IL-2 had become sensitive to Fas induced apoptosis with over 90% apoptosis induced by CH11. FLIP expression was analyzed by RTPCR. 10×106 CD4+ lymphocytes were used per sample. RNA was isolated using Trizol. Reverse transcription was performed using MMRV and the samples were run in a polymerase chain reaction using primers designed for the human FLIP. Parallel samples were run with B-Actin. The products were then run on agarose gels stained with ethidium bromide. FLIP was not present in unactivated human CD4+ lymphocytes. Expression increased over time following activation and was maximal at 6 days. In the presence of high doses of IL-2 (100 units) FLIP expression was downregulated. The down regulation of FLIP was not seen following activation when lower doses of IL-2 were used. Our results suggest that FLIP is regulated by IL-2 and that this may play a role in IL-2 mediated effects on activation induced cell death. Given the central role of FLIP in the death cascade this may provide a point of manipulation of the death pathway.
High-order statistical equalizer for nonlinearity compensation in dispersion-managed coherent optical communications (2012)

Fiber nonlinearity has become a major limiting factor to realize ultra-high-speed optical communications. We propose a fractionally-spaced equalizer which exploits a trained high-order statistics to deal with data-pattern dependent nonlinear impairments in fiber-optic communications. The computer simulation reveals that the proposed 3-tap equalizer improves Q-factor by more than 2 dB for long-haul transmissions of 5,230 km distance and 40 Gbps data rate. We also demonstrate that the joint use of a digital backpropagation (DBP) and the proposed equalizer offers an additional 1-2 dB performance improvement due to the channel shortening gain. A performance in high-speed transmissions of 100 Gbps and beyond is evaluated as well.