gebhart/patrepeval huggingface dataset:
Nickel‐Catalyzed Benzylic CH Functionalization (2022)

Abstract Nickel‐catalyzed CH functionalization has emerged as a powerful tool for the sustainable synthesis of strategic organic molecules. While many efforts have focused on the functionalization of C(sp 2 )H bond on arenes and heteroarenes in past decades, much less research has been devoted to the activation and functionalization of challenging benzylic C(sp 3 )H bonds. This article highlights the development in the area of benzylic C(sp 3 )H functionalization, with a particular emphasis on reaction development, scope, and reaction mechanism.
A 0&#x2013;1 program to form minimum cost clusters in the downlink of cooperating base stations (2012)

Base station cooperation in the downlink of cellular systems has been recently suggested as a promising concept towards a better exploitation of the communication system's physical resources. It may offer a high gain in capacity through interference mitigation. This however, comes at a cost of high information exchange between cooperating entities and a high computational burden. Clustering of base stations into subgroups is an alternative to guarantee such cooperation benefits in a lower scale. The optimal definition of clusters, however, and a systematic way to find a solution to such problem is not yet available. In this work, we highlight the combinatorial nature of the problem, exploit this to describe the system of users and base stations as a graph and formulate a pure 0-1 program. Its solution suggests a cost optimal way to form clusters and assign user subsets to them.
Supplementary Figure 3 from Therapeutic Efficacy of an Fc-Enhanced TCR-like Antibody to the Intracellular WT1 Oncoprotein (2023)

&lt;p&gt;PDF file - 183KB, (A) ESKM reduced individual tumor burden during the treatment course in 3 of 5 mice. Alternate representation of data in Figure 2A, where signal for each mouse is normalized to starting luminescence. (B) ESKM had no effect against JMN in a NOG mouse model. (C) Comparison of BV173 (Ph+ ALL) and SET2 (AML) cell lines in NSG mice.&lt;/p&gt;
Monotype Organic Dual Threshold Voltage Using Different OTFT Geometries (2019)

It is well known that organic thin film transistor (OTFT) parameters can be shifted depending on the geometry of the device. In this work, we present two different transistor geometries, interdigitated and Corbino, which provide differences in the key parameters of devices such as threshold voltage (VT), although they share the same materials and fabrication procedure. Furthermore, it is proven that Corbino geometries are good candidates for saturation-mode current driven devices, as they provide higher ION/IOFF ratios. By taking advantage of these differences, circuit design can be improved and the proposed geometries are, therefore, particularly suited for the implementation of logic gates. The results demonstrate a high gain and low hysteresis organic monotype inverter circuit with full swing voltage at the output.
Capability of DUV inspection for the LWR improved EUV mask of sub-15 nm hp on wafer (2019)

Deep Ultra Violet (DUV) inspection of Extreme Ultra Violet (EUV) mask has been known for high stability, high throughput, and low cost, since it has been used for a long time, even though sensitivity is thought to be insufficient for the EUV mask of under 20 nm half pitch (hp). We have been studying extendibility for 1X nm hp of the DUV inspection using optics named Super Inspection Resolution Improvement method for UnreSolved pattern (SIRIUS). In previous study, we demonstrated the DUV inspection has capability for the EUV mask of 17 nm hp Lines and Spaces (LS) on wafer. In this paper, the more extendibility for the DUV inspection of EUV masks under sub-15 nm on wafer was demonstrated by studying relationship of roughness and sensitivity. Firstly, an estimated model for effects of the EUV mask roughness to Signal Noise Ratio (SNR) of the inspection image was established, and simulation was carried out. Secondly, the SNR was evaluated using actual Line Width Roughness (LWR) improved masks. It was confirmed that the results are the same trend as the model and the simulation, and, the SNR is enhanced with the LWR improvement. Finally, the sensitivity of the LWR improved mask was evaluated. As a result, it becomes enough for the EUV mask over 13 nm hp on wafer. In conclusion, we confirm that the DUV inspection of the EUV mask by the SIRIUS can be extending to the 13 nm hp LS on wafer, this is around the limit of NA 0.33 EUV lithography, using the LWR improved mask.
Clostridioides difficile para -Cresol Production Is Induced by the Precursor para -Hydroxyphenylacetate (2020)

<i>Clostridioides difficile</i> is an etiological agent for antibiotic-associated diarrheal disease. <i>C. difficile</i> produces a phenolic compound, <i>para</i>-cresol, which selectively targets gammaproteobacteria in the gut, facilitating dysbiosis. <i>C. difficile</i> decarboxylates <i>para</i>-hydroxyphenylacetate (<i>p</i>-HPA) to produce <i>p</i>-cresol by the action of the HpdBCA decarboxylase encoded by the <i>hpdBCA</i> operon. Here, we investigate regulation of the <i>hpdBCA</i> operon and directly compare three independent reporter systems; SNAP-tag, glucuronidase <i>gusA</i>, and alkaline phosphatase <i>phoZ</i> reporters to detect basal and inducible expression. We show that expression of <i>hpdBCA</i> is upregulated in response to elevated <i>p</i>-HPA. <i>In silico</i> analysis identified three putative promoters upstream of <i>hpdBCA</i> operon-P<sub>1</sub>, P<sub>2</sub>, and Pσ<sup>54</sup>; only the P<sub>1</sub> promoter was responsible for both basal and <i>p</i>-HPA-inducible expression of <i>hpdBCA</i> We demonstrated that turnover of tyrosine, a precursor for <i>p</i>-HPA, is insufficient to induce expression of the <i>hpdBCA</i> operon above basal levels because it is inefficiently converted to <i>p</i>-HPA in minimal media. We show that induction of the <i>hpdBCA</i> operon in response to <i>p</i>-HPA occurs in a dose-dependent manner. We also identified an inverted palindromic repeat (AAAAAG-N<sub>13</sub>-CTTTTT) upstream of the <i>hpdBCA</i> start codon (ATG) that is essential for inducing transcription of the <i>hpdBCA</i> operon in response to <i>p</i>-HPA, which drives the production of <i>p</i>-cresol. This provides insights into the regulatory control of <i>p</i>-cresol production, which affords a competitive advantage for <i>C. difficile</i> over other intestinal bacteria, promoting dysbiosis.<b>IMPORTANCE</b><i>Clostridioides difficile</i> infection results from antibiotic-associated dysbiosis. <i>para</i>-Cresol, a phenolic compound produced by <i>C. difficile</i>, selectively targets gammaproteobacteria in the gut, facilitating dysbiosis. Here, we demonstrate that expression of the <i>hpdBCA</i> operon, encoding the HpdBCA decarboxylase which converts <i>p</i>-HPA to <i>p</i>-cresol, is upregulated in response to elevated exogenous <i>p</i>-HPA, with induction occurring between >0.1 and ≤0.25 mg/ml. We determined a single promoter and an inverted palindromic repeat responsible for basal and <i>p</i>-HPA-inducible <i>hpdBCA</i> expression. We identified turnover of tyrosine, a <i>p</i>-HPA precursor, does not induce <i>hpdBCA</i> expression above basal level, indicating that exogenous <i>p</i>-HPA was required for <i>p</i>-cresol production. Identifying regulatory controls of <i>p</i>-cresol production will provide novel therapeutic targets to prevent <i>p</i>-cresol production, reducing <i>C. difficile</i>'s competitive advantage.
Performance Evaluation of Cell Search Time for Heterogeneous Networks (2014)

This paper proposes local cell cluster-specific primary synchronization signal (PSS) sequence assignment and local cell-specific secondary synchronization signal (SSS) sequence assignment schemes for orthogonal frequency division multiple access (OFDMA) heterogeneous networks. The proposed synchronization signal (SS) sequences are based on those of the Long-Term Evolution (LTE) radio interface. We investigate the effects of the proposed SS sequence assignments from the viewpoint of the initial cell search time for various inter-cell site synchronization modes based on system-level simulations. We show that the local cell cluster-specific PSS sequence assignment achieves fast cell search time performance that is almost the identical level to that assuming the cell arrangement with a macrocell only. We show, however, that the effect of the new local cell-specific SSS sequences based on cyclic-shifted M-sequence in addition to the current 168 SSS sequences is small from the viewpoint of reducing the initial cell search time.
Study of Raman effect of ultrashort pulse in optical fiber (2005)

The Raman effect influence on ultrashort pulse in optical fiber is investigated by using experimental data of delay response function. The frozen of the Raman effect is clarified by using nonlinear Schrodinger equation and finite difference time domain method. In Raman freezing region, a more stable soliton propagation is obtained when the initial power is enhanced.
A high-drive, high-swing buffer amplifier (1991)

A CMOS high dynamic range, high-drive buffer suitable for driving large capacitive loads is presented. A new area-efficient output stage has been used so that simulations reveal a drive capability of 200 kHz into a 5000-pF load. The circuit occupies only 110 mils/sup 2/ in a 3- mu m technology. The output range is rail to rail for R>10 k Omega . The buffer is capable of driving resistive loads down to 300 Omega with acceptable total harmonic distortion (THD).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
GENETIC TRANSFORMATION A ND H YBRIDIZATION (2006)

Efficient production of seedling-derived Type I callus was demonstrated for several corn genotypes in- cluding commercial inbred lines. Seeds were germinated on MS-based medium containing 10 mg l −1 picloram and 3m g l −1 6-benzylaminopurine, which induced the devel- opment of axillary buds in the area of coleoptilar node. Nodal sections of 7-10-day old seedlings were isolated, split longitudinally, and placed on callus induction medium supplemented with 2.2 mg l −1 picloram and 0.5 mg l −1 2,4- dichlorophenoxyacetic acid. For lines L4 and L9 the fre- quency of embryogenic callus induction was 38-42% based on calli per split nodal section. Frequency of callus induc- tion from split nodal sections of seeds germinated on media without growth regulators was 0-3%. Seedling-derived cal- lus of five genotypes was used for Agrobacterium-mediated transformation. Two constructs containing the green fluo- rescence protein gene and genes for either neomycin phos- photransferase II or glyphosate selection were used in trans- formation experiments. Transformation frequency varied from 2 to 11% and about 60% of the T0 plants had 1-2 copies of transgenes.
Semi-automated 3D segmentation of human skeletal muscle using Focused Ion Beam-Scanning Electron Microscopic images (CA1 Hippocampal Tissue) (2019)

Segmentation of CA1 Hippocampal tissue test dataset from Lucchi et al. 2013. Containing Mitochondrial, Filament and Cytosol/Cell membrane files both low and high resolution (10.8 GB Uncompressed).
Performance measurements of the X window system communication protocol (1990)

The X Window System® is a portable, network transparent window system. An X server manages the resources of an X display consisting of a screen, keyboard and pointer. An X server distributes user input (events) to and accepts output (requests) from X clients which vie for display resources. X provides an environment in which servers and clients may be separated by a communications network so that application programs can use graphical interfaces on remote hosts. Servers and clients communicate through a well-defined protocol that in turn uses protocols like the Internet TCP/IP protocol suite as a transport mechanism. Separation of servers and clients by a network introduces the possibility of performance degradation due to communication delays. These delays may be either due to latency resulting from round-trip delays between servers and clients or transmission delays resulting from the volume of traffic through the communications network. The X protocol is rigidly defined at a fairly low level, so that some forms of interaction between servers and clients may require the exchange of many events and requests through the underlying transport protocol across the communications network. Thus, there are many opportunities for network communication delays to affect the execution of X programs. This paper investigates the resources required by the X protocol from the communications network to evaluate the potential for communications delays induced by X protocol traffic. A protocol analysis tool, xlog, monitors the use of the communications protocol between a server and clients, and records a log of protocol messages for post-mortem analysis. We present the results of measurements of the X protocol taken with xlog for a variety of X clients and servers communicating over a 10Mb per second Ethernet. Although the overall network usage observed was not overly high, clients and servers using the X protocol did exhibit bursty behaviour in which transitory bandwidth requirements were significant. Some X applications may induce a significant load on the communications resources provided by an Ethernet. Applications developers and network architects must be aware of the load caused by the X protocol when designing networked graphic systems.
[Gd(Try-TTDA)(H2O)]2−: A new MRI contrast agent for copper ion sensing (2011)

In this study, we have developed two new L-tryptophan based contrast agents [Gd(Try-TTDA)(H(2)O)](2-) and [Gd(Try-ac-DOTA)(H(2)O)](-). Upon addition of Cu(II) to [Gd(Try-TTDA)(H(2)O)](2-), significant increases in the relaxivity (r(1)) and hydration number of [Gd(Try-TTDA)(H(2)O)](2-) were observed. However, it only induced a minute increase in the relaxivity (r(1)) in the case of [Gd(Try-ac-DOTA)(H(2)O)](-). Furthermore, the interaction of Cu(II) with the indole ring of Gd(III) complexes was explored by measuring the intrinsic fluorescence of the tryptophan of the Gd(III) complex. With the addition of one equivalent of Cu(II) to [Gd(Try-TTDA)(H(2)O)](2-) the indole fluorescence was completely quenched. Moreover, the [Gd(Try-TTDA)(H(2)O)](2-) complex shows excellent selectivity towards Cu(II) over other metal ions (Cu(II) > La(III) > Mg(II)). Importantly, the significant signal intensity (2073 ± 67) for in vitro MR imaging using [Gd(Try-TTDA)(H(2)O)](2-) in the presence of Cu(II) implicates that this new smart contrast agent ([Gd(Try-TTDA)(H(2)O)](2-)) can serve as a Cu(II) sensor for MR imaging.
Analysis of Light Leakage Caused by Color Filter between Crossed Polarizers (2007)

The light leakage caused by color filters between crossed polarizers was analyzed in terms of light scattering due to pigments inside color filter layers. Localized pigment particles in the color filter layers used in devices were observed with a scanning transmission electron microscope. The direct observation of the scattering light revealed that the pigment particles cause Rayleigh scattering. We found that the depolarized light leakage by color filters between crossed polarizers is governed by light scattering.
Reactions of small carbon clusters with water in cryogenic matrixes: the FTIR spectrum of hydroxyethynyl carbene (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of small carbon clusters with water in cryogenic matrixes: the FTIR spectrum of hydroxyethynyl carbeneBryan J. Ortman, Robert H. Hauge, John L. Margrave, and Zakya H. KafafiCite this: J. Phys. Chem. 1990, 94, 20, 7973–7977Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/j100383a041https://doi.org/10.1021/j100383a041research-articleACS PublicationsRequest reuse permissionsArticle Views158Altmetric-Citations29LEARN 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 options Get e-Alerts
Convergence analysis of the information matrix in Gaussian belief propagation (2017)

Gaussian belief propagation (BP) has been widely used for distributed estimation in large-scale networks such as the smart grid, communication networks, and social networks, where local measurements/observations are scattered over a wide geographical area. However, the convergence of Gaus- sian BP is still an open issue. In this paper, we consider the convergence of Gaussian BP, focusing in particular on the convergence of the information matrix. We show analytically that the exchanged message information matrix converges for arbitrary positive semidefinite initial value, and its dis- tance to the unique positive definite limit matrix decreases exponentially fast.
Polymorphisms inInterleukin-6-6331 Influences the Susceptibility of a Chinese Population to Gastric Cancer (2011)

We investigated the association of Interleukin (IL)-6-6331 polymorphisms with susceptibility to gastric cancer in 375 patients with gastric cancer and 386 age-and gender-matched healthy controls. After adjustment for the potential confounding effects of gender and age, IL-6-6331TC genotype was associated with a decreased risk of gastric cancer compared with the CC genotype. Further stratification analyses indicated that the protective effect of TC genotype was also observed in poorly differentiated gastric cancer, noncardia gastric cancer, and intestinal-type gastric cancer, respectively. These results suggest that the IL-6-6331 polymorphism is involved in susceptibility to developing gastric cancer. © 2011 Informa Healthcare USA, Inc.
LINE-1 expression in cancer correlates with DNA damage response, copy number variation, and cell cycle progression (2020)

ABSTRACT Retrotransposons are genomic DNA sequences that are capable of copying themselves to new genomic locations via RNA intermediates; LINE-1 is the only retrotransposon that remains autonomous and active in the human genome. The mobility of LINE-1 is largely repressed in somatic tissues, but LINE-1 is active in many cancers. Recent studies using LINE-1 constructs indicate that host cells activate a DNA damage response (DDR) to repair retrotransposition intermediates and resolve conflicts between LINE-1 and DNA replication. Using multi-omic data from the CPTAC project, we found correlations between LINE-1 expression and ATM-MRN-SMC DDR signalling in endometrial cancer and between LINE-1 and the ATR-CHEK1 pathway in p53 wild type breast cancer. This provides evidence that conflicts between LINE-1 and DNA replication occur in at least some human cancers. Furthermore, LINE-1 expression in these cancers is correlated with the total amount of copy number variation genome wide, indicating that, when active in cancer, pointing to a direct impact of LINE-1 associated DNA damage on genome structure. We also find that, in endometrial and ovarian cancer, LINE-1 expression is correlated with the expression of genes that drive cycle progression including E2F3, PLK1 and Aurora kinase B. This study provides evidence, supporting recent work in model cell lines, of a LINE-1/DDR connection in human tumors and raises the possibility of additional interactions between LINE-1 and the cell cycle.
The RUDY study platform – a novel approach to patient driven research in rare musculoskeletal diseases (2016)

The strengths of RUDY include low burden for the clinical team, low research administration costs with high participant recruitment and ease of data collection and access. This platform has the potential to be used as the model for other rare diseases globally.
MPI on IBM SP1/SP2: current status and future directions (2002)

A complete prototype implementation of MPI on the IBM Scalable Power PARALLEL 1 and 2 (SP1, SP2) is discussed. This implementation achieves essentially the same performance as the native EUI library, although MPI is much larger. The paper describes the implementation of EUI on SP1/SP2, and the modifications required to to implement MPI, initial performance measurements, and directions for future work.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abstract P3-04-01: Protein pathway activation mapping of the I-SPY 1 biopsy specimens identifies new network focused drug targets for patients with triple negative tumors (2012)

Abstract Background: Identification of new therapies and predictive biomarkers is needed for patients with triple negative (TN) breast cancer. Elucidating pathway activation in cancer is critical as these proteins represent targets for many of the new molecular therapeutics and companion diagnostic markers. The I-SPY TRIAL (CALGB 150007/150012, ACRIN 6657) is a trial of neoadjuvant anthracycline- and taxane-based chemotherapy that provides longitudinal biopsy specimens and molecular and clinical/pathological characterization. Methods: Tumor epithelium was procured by Laser Capture Microdissection from 149 pretreatment frozen biopsy specimens (T1) and 102 frozen biopsy specimens collected 1–4 days after first chemotherapy treatment (T2). Reverse Phase Protein Microarray was used to measure the activation of 39 and 100 signaling proteins in the T1 and T2 biopsies, respectively, including drug targets for Phase I-III and FDA cleared therapeutics. Associations between pathway activation and response to chemotherapy (RCB 0/1 vs. 2/3) and relapse-free survival (RFS) were evaluated for the triple-negative (TN) patient population at each time point and for changes between T1 and T2. Significance thresholds for response and RFS were as follows: Wilcoxon rank sum test p &amp;lt; 0.05; Cox proportional hazard model, likelihood ratio p &amp;lt; 0.05. Results: We focused our analysis on protein changes in patients who had poor clinical outcomes (Table 1) We observed systemic activation of receptor tyrosine kinases such as MET and ALK in the T2 biopsies from patients that recurred, and VEGFR activation was seen in the T1 relapsed tumors. Activation in the AURORA-PLK1 cell cycle signaling network was seen with increased activation in the T2 biopsy from patients who did not respond to therapy and had poor RFS. Dynamic changes in ERK activation were revealed with decreased ERK activation between T1 and T2 time points associated with recurrence. Conclusions: Our analysis has revealed activation and increased expression of proteins involved in proliferation (Ki67), DNA repair (phosphorylated p53) and protein kinases in patients with TN disease who had poor clinical response. These events, if validated, point to potential treatment options that could be considered for non-responding TN breast cancer patients. VEGFR, ALK and MET, have FDA cleared therapeutics that could be rationally proposed for rapid clinical investigation, and there are numerous investigational agents that target AURORA and PLK1 in the clinic. Further validation is required to explore the significance of these ongoing findings with the hope that the analysis could lead to molecularly rationalized therapies for patients with TN tumors. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-04-01.