gebhart/patrepeval huggingface dataset:
2P-179 3D force detection in optical tweezers : application to molecular motors(The 46th Annual Meeting of the Biophysical Society of Japan) (2008)

Durillg the weak binding state the motol hLdd exhibits Biowman motion alons a rnicrotubule {MT) un"1 it tmds th" next bmdmg gitL Thug the mechamsm of the one dimLflyonal (1D) Browniaii metiop is important for moulity he"eNer it hag "ot yLt understood thL mLLhanisrn that rndkcs the snrmILaneous binding and ]novement possiblc Tn eur previou-studM ID Bro"mian motson along MTs was simulated by usmg pos]inxeLy charged pelyacry]amide partieles (drameter 'v25 nm) indicatmg thdt tubulin gpecihu binding was not TeqQirLd to maintain the rnotion Further quantstative analysis reNealcd that the paitiLkb repeatediy bound to and jumped betweui the potenttal holes along the MTs dnrmg the 1D Brownian rnotion The4 how ts the potential profik along MTK determinedO What exactly ib the structural emtity of the petentiaL holes?To address thege questions ill thig gtudy we have gLllLrated mutant MTb wtth variable chargL densities or distrtbutionts at the glutanllne nch C terminal region of tubuhn dnd tested thL ID Brewnian motion ofthe chargedparticles that movLd along thetse mutanit MTts On the basis et this anaJysis we expect to Llucidate the role of the C termmal region on the bmding amd jumpmg durmg the ID Brovvmdn motuon ThL analysis is underway and we will rqport the results m a pogtcr photochrorme compoundg We have previougty demonstrated that ABDM "as inuorpoiated mto thL funcuonal site of siceletal muscle myosm head (Sl) and the g}obal Lonformational changc ef S1 was mduLLd by eis trans isornLri7atson ofthe cross lmkLd ABT]M upon UVVIS 1ight madiation whiLh may mimic thL Lonformational change atcomptnied by LnLrgy transduction "le have also cToss hnked kmesin using ABDM in order to photo LontroL the rvrPage dctwity ef ]"nesm WL have prepared the mutants of ktnesm motor domain T242C A244C A247C J 249C, A252C CJ272C aiid S275C, which hdvL d smgte eystcmL rLbiduL m Ll1 oT LI2 Only A2S2C crobs hnked by ABDM bhowed signifiLdnt a]teration of MPagc dLtivit} upou UV and VIS light irrackation In the piesent study "e prLparLd novel rnutants ot lanesm motor demam A21C R2SC G26C m Ll bmd]ng gite QI04C in AJ'P bindmg sitL TI96C mI9 T273C K274C H276C m Ll2 to regulate MPase aLtivity Lfflciently Thc mutdntb weTe cross lmked mtermoleLulaily by ABDM at high efficiencv 7090% These mutants cross 1inkLd by ABDM shovved alteration of mease aLtivity between UV aiid VIS 1ight llradiation EspeLidlly thL kmegin mutdnt A252C was rLgulated most effectively 2P-174 P*vY2SasOnt/1acOeszz.NcoATPvaaOaa{ic ObstrNd"onofIYTPbind]ngtotheind]vidualrnotordornainsofdimLrickmebin MaoLmg(ij pmei ldbnreJ MichikobakalTmaav Wichio ibntishigea) Q) a Deparrment ofBioengmeeting School ofEnginLLnng bntverstCF of rblyo 2 Dcparlment ofAlzphLci Plysi" SchoolofEngtnLrnns bn"ersityof7blyoj Kmesm ig a diinenc motor protem that moves along miLrotubules m a hand over hand manner by hydro!yi]ng MP
A Tiling Approach to Network Code Design for Wireless Networks (2006)

We describe a new tiling approach for network code design. The proposed method applies dynamic programming to find the best strategy among a restricted collection of network codes. We demonstrate the proposed strategy as a method for efficiently accommodating multiple unicasts in a wireless coding environment on a triangular lattice and discuss its generalization.
Supplementary Figure S4 from Targeting DNA Damage Repair Functions of Two Histone Deacetylases, HDAC8 and SIRT6, Sensitizes Acute Myeloid Leukemia to NAMPT Inhibition (2023)

&lt;p&gt;Mutant IDH1/2 enhances AR-42/KPT-9274 combination sensitivity in a 2-HG-dependent manner.&lt;/p&gt;
Preferential Expression of MUC6 in Oncocytic and Pancreatobiliary Types of Intraductal Papillary Neoplasms Highlights a Pyloropancreatic Pathway, Distinct From the Intestinal Pathway, in Pancreatic Carcinogenesis (2010)

(1) The expression of MUC6 in oncocytic and pancreatobiliary-type neoplasms but not in villous or intestinal-type neoplasms supports the presence of a pyloropancreatic pathway distinct from the MUC2/CDX2 expressing intestinal pathway in intraductal papillary neoplasia. (2) MUC6 expression is present in the earliest (nonpapillary) form of any type of preinvasive neoplasia regardless of whether it is PanIN or IOPN or IPMN or MCN suggesting that these entities may share some characteristics early on, but evolve along divergent pathways as they progress.
Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence (2017)

Mycobacterium tuberculosis (MTb) is the causative agent of pulmonary tuberculosis (TB). MTb colonizes the human lung, often entering a non-replicating state before progressing to life-threatening active infections. Transcriptional reprogramming is essential for TB pathogenesis. In vitro, Cmr (a member of the CRP/FNR super-family of transcription regulators) bound at a single DNA site to act as a dual regulator of cmr transcription and an activator of the divergent rv1676 gene. Transcriptional profiling and DNA-binding assays suggested that Cmr directly represses dosR expression. The DosR regulon is thought to be involved in establishing latent tuberculosis infections in response to hypoxia and nitric oxide. Accordingly, DNA-binding by Cmr was severely impaired by nitrosation. A cmr mutant was better able to survive a nitrosative stress challenge but was attenuated in a mouse aerosol infection model. The complemented mutant exhibited a ∼2-fold increase in cmr expression, which led to increased sensitivity to nitrosative stress. This, and the inability to restore wild-type behaviour in the infection model, suggests that precise regulation of the cmr locus, which is associated with Region of Difference 150 in hypervirulent Beijing strains of Mtb, is important for TB pathogenesis.
Quantum computing using Cirq and OpenFermion with application to quantum chemistry (2020)

This workshop will introduce Google's API for programming and using quantum computers, known as Cirq. We will discuss the basics of how to use Cirq and the philosophy behind its design, and also demonstrate how the framework can be used in conjunction with the open source package OpenFermion to perform small scale quantum chemistry simulations.
Convergence analysis and experiments using an RPEM based on nonlinear ODEs and midpoint integration (2012)

A convergence analysis is performed for a recursive prediction error algorithm based on nonlinear ODEs and the midpoint integration algorithm. Several conditions are formulated such that the stability of an associated differential equation can be tied to the local and global convergence properties of the algorithm. This is used to show that the algorithm converges to a minimum point of the criterion function, which may or may not be unique. A consequence is that convergence to the true parameters is possible. As compared to previous work, complete system assumptions are integrated in the analysis, thereby generalising previous results. The theoretical analysis of this paper is complemented with numerical examples and with live data experiments.
Microphase Segregation in the Melts of Bottlebrush Block Copolymers (2020)

We present an analytical theory of microphase separation in the melt of bottlebrush and comblike block copolymers in the strong segregation limit. The constructed phase diagram predicts morphologies and dimensions of the microsegregated domains as a function of molecular masses of both blocks, grafting densities and lengths of side chains in the comblike and bottlebrush blocks. The theoretical predictions are corroborated by experimental data.
The Effects of Selective Hematopoietic Expression of Human IL-37 on Systemic Inflammation and Atherosclerosis in LDLr-Deficient Mice (2017)

The human cytokine interleukin (IL)-37 has potent anti-inflammatory capacities, and hematopoietic cell-specific transgenic overexpression of IL-37 in mice protects against septic shock and colitis. In the present study we investigated the effect of hematopoietic expression of IL-37 on atherosclerosis development under low-grade inflammatory conditions. Low-density lipoprotein receptor (LDLr)-deficient mice were lethally irradiated and transplanted with bone marrow from IL-37-transgenic or control wild-type mice and fed a Western-type diet (WTD; 1% cholesterol) for eight weeks. Metabolic and inflammatory parameters were monitored and atherosclerosis was assessed in the aortic valve area. Hematopoietic IL-37 expression did not influence body weight, food intake and plasma cholesterol levels during the study. Plasma soluble E-selectin levels were increased with WTD-feeding as compared to chow-feeding, but were not influenced by IL-37 expression. IL-37 expression reduced the inflammatory state as indicated by reduced white blood cell counts and by reduced basal and lipopolysaccharide-induced cytokine response by peritoneal macrophages ex vivo. IL-37 expression did not influence the atherosclerotic lesion area. Lesion composition was marginally affected. Smooth muscle cell content was decreased, but macrophage and collagen content were not different. We conclude that under low-grade inflammatory conditions, hematopoietic IL-37 expression reduces the inflammatory state, but does not influence atherosclerosis development in hyperlipidemic LDLr-deficient mice.
High Frequency Confinement Factor Modulation of Diode Lasers (1997)

In this paper we discuss the possibility of confinement factor and dual (confinement &amp; pumping current) modulation of laser diodes. In the initial experiment, four-terminal Fabry–Pérot lasers of ridge guide type with two additional side electrodes were tested. The possibility of controlling the lateral part of the optical confinement factor by applying an external voltage to the side contacts was proved in this experiment. To analyze the dynamic behavior of the four-terminal laser under confinement factor and dual modulation, a simple model and a more accurate new model were developed, the last one based on the simultaneous solution of laser rate equations and matrix equation relating potentials and currents. The simulations carried out on the basis of the advanced model allowed us to propose an optimized four-terminal laser structure promising enhanced performance under dual modulation. It is shown that dual modulation may result in very efficient correction of output waveforms which leads to a much better opening of transmitted eye patterns at high bit rates as compared to direct modulation.
SCF ubiquitin protein ligases and phosphorylation–dependent proteolysis (1999)

Many key activators and inhibitors of cell division are targeted for degradation by a recently described family of E3 ubiquitin protein ligases termed Skp1-Cdc53-F-box protein (SCF) complexes. SCF complexes physically link substrate proteins to the E2 ubiquitin-conjugating enzyme Cdc34, which catalyses substrate ubiquitination, leading to subsequent degradation by the 26S proteasome. SCF complexes contain a variable subunit called an F-box protein that confers substrate specificity on an invariant core complex composed of the subunits Cdc34, Skp1 and Cdc53. Here, we review the substrates and pathways regulated by the yeast F-box proteins Cdc4, Grr1 and Met30. The concepts of SCF ubiquitin ligase function are illustrated by analysis of the degradation pathway for the G1 cyclin Cln2. Through mass spectrometric analysis of Cdc53 associated proteins, we have identified three novel F-box proteins that appear to participate in SCF-like complexes. As many F-box proteins can be found in sequence databases, it appears that a host of cellular pathways will be regulated by SCF-dependent proteolysis.
MSE bounds dominating the cramer-RAO bound (2005)

Traditional Cramer-Rao type bounds provide benchmarks on the variance of any estimator of a deterministic parameter vector, while requiring a priori specification of a desired bias gradient. However, in applications, it is often not clear how to choose the required bias. A direct measure of the estimation error that takes both the variance and the bias into account is the mean-squared error (MSE). Here, we develop bounds on the MSE in estimating a deterministic vector x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> using estimators with linear bias vectors, which includes the traditional unbiased estimation as a special case. We show that there often exists linear bias vectors that result in an MSB bound that dominates the CRLB, so that it is smaller than the CRLB for all x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0 </sub> . Furthermore, we explicitly construct estimators that achieve these bounds by linearly transforming the maximum-likelihood estimator
Improvement of RG1-VLP vaccine performance in BALB/c mice by substitution of alhydrogel with the next generation polyphosphazene adjuvant PCEP (2021)

Current human papillomavirus (HPV) vaccines provide substantial protection against the most common HPV types responsible for oral and anogenital cancers, but many circulating cancer-causing types remain for which vaccine coverage is lacking. In addition, all current HPV vaccines rely on aluminum salt-based adjuvant formulations that function through unclear mechanisms with few substitutes available. In an effort to expand the toolbox of available adjuvants suitable for HPV vaccines, we compared the immunogenicity of the RG1-VLP (virus-like particle) vaccine in BALB/c mice when formulated with either the aluminum hydroxide adjuvant Alhydrogel or the novel polyphosphazene macromolecular adjuvant poly[di (carboxylatoethylphenoxy) phosphazene] (PCEP). PCEP-formulated RG1-VLPs routinely outperformed VLP/Alhydrogel in several measurements of VLP-specific humoral immunity, including consistent improvements in the magnitude of antibody (Ab) responses to both HPV16-L1 and the L2 RG1 epitope as well as neutralizing titers to HPV16 and cross-neutralization of pseudovirion (PsV) types HPV18 and HPV39. Dose-sparing studies indicated that RG1-VLPs could be reduced in dose by 75% and the presence of PCEP ensured activity comparable to a full VLP dose adjuvanted by Alhydrogel. In addition, levels of HPV16-L1 and -L2-specific Abs were achieved after two vaccinations with PCEP as adjuvant that were equivalent to or greater than levels achieved with three vaccinations with Alhydrogel alone, indicating that the presence of PCEP resulted in accelerated immune responses that could allow for a decreased dose schedule. Given the extensive clinical track record of polyphosphazenes, these data suggest that substitution of alum-based adjuvants with PCEP for the RG1-VLP vaccine could lead to rapid seropositivity requiring fewer boosts, the dose-sparing of commercial VLP-based vaccines, and the establishment of longer-lasting humoral responses to HPV.
Engine Mount Design Strategies to Mitigate Linear Vibrations in a Tata Nano (2018)

In 2009, Tata Motors launched the Tata Nano as a low-cost alternative to two and three-wheeled vehicles for India’s growing middle class. However, the Nano failed to meet these expectations as it developed a negative perception amongst Indian consumers partly due to its poor Noise Vibration Harshness (NVH) characteristics. In this paper, we examine strategies to reduce the transmission of linear vibrations from the engine felt inside the cabin. Specifically, it includes analysis of the hardness of damping rubber in the engine mounts as well as geometry of the engine mounts. The results of this analysis suggest that Tata Motors can reduce the vibrations transmitted from the engine by decreasing the hardness of the damping rubber. Additionally, Tata Motors can further reduce the transmitted vibrations by decreasing mount angle. It was found that a reduction in mount angle from 45° to 30° reduced the amplitude of the transmitted vibrations by 23%.
Pathology of Breast and Ovarian Cancers among BRCA1 and BRCA2 Mutation Carriers: Results from the Consortium of Investigators of Modifiers of BRCA1 / 2 (CIMBA) (2012)

There was strong evidence that the proportion of estrogen receptor (ER)-negative breast tumors decreased with age at diagnosis among BRCA1 (P-trend = 1.2 × 10(-5)), but increased with age at diagnosis among BRCA2, carriers (P-trend = 6.8 × 10(-6)). The proportion of triple-negative tumors decreased with age at diagnosis in BRCA1 carriers but increased with age at diagnosis of BRCA2 carriers. In both BRCA1 and BRCA2 carriers, ER-negative tumors were of higher histologic grade than ER-positive tumors (grade 3 vs. grade 1; P = 1.2 × 10(-13) for BRCA1 and P = 0.001 for BRCA2). ER and progesterone receptor (PR) expression were independently associated with mutation carrier status [ER-positive odds ratio (OR) for BRCA2 = 9.4, 95% CI: 7.0-12.6 and PR-positive OR = 1.7, 95% CI: 1.3-2.3, under joint analysis]. Lobular tumors were more likely to be BRCA2-related (OR for BRCA2 = 3.3, 95% CI: 2.4-4.4; P = 4.4 × 10(-14)), and medullary tumors BRCA1-related (OR for BRCA2 = 0.25, 95% CI: 0.18-0.35; P = 2.3 × 10(-15)). ER-status of the first breast cancer was predictive of ER-status of asynchronous contralateral breast cancer (P = 0.0004 for BRCA1; P = 0.002 for BRCA2). There were no significant differences in ovarian cancer morphology between BRCA1 and BRCA2 carriers (serous: 67%; mucinous: 1%; endometrioid: 12%; clear-cell: 2%). CONCLUSIONS/IMPACT: Pathologic characteristics of BRCA1 and BRCA2 tumors may be useful for improving risk-prediction algorithms and informing clinical strategies for screening and prophylaxis.
ChemInform Abstract: Gold Catalysts Prepared by Coprecipitation for Low‐Temperature Oxidation of Hydrogen and of Carbon Monoxide. (1989)

Abstract Novel gold catalysts are prepared by coprecipitation from aqueous HAuCl 4 solutions containing nitrates of various transition metals (Mn, Fe, Co, Ni, Cu).
Quetiapine Carboxylic Acid and Quetiapine Sulfoxide Prevalence in Patient Urine (2016)

Treatment adherence is often an issue with mental health patients. For those prescribed quetiapine (Seroquel<sup>®</sup>), the low levels of parent drug and plasma metabolite(s) (e.g., 7-hydroxyquetiapine) typically used in urine drug monitoring can result in false negatives with concomitant unfavorable impacts on patient care. Literature review coupled with liquid chromatography/time-of-flight mass spectrometry analysis of patient positive urine samples indicated the presence of quetiapine carboxylic acid and quetiapine sulfoxide as significant urinary metabolites of quetiapine. Analysis of these two metabolites determined that they are abundant in the urine of quetiapine patients and can result in apparent adherence rates that are improved relative to those determined using only quetiapine and 7-hydroxyquetiapine. For example, analysis of a random set of 114 patients who were prescribed quetiapine exhibited an apparent adherence rate of 47% using the quetiapine carboxylic acid and quetiapine sulfoxide metabolites. Traditional metabolite testing with quetiapine and 7-hydroxyquetiapine yielded apparent adherence rates of ~31% while all four analytes resulted in apparent adherence of 48%. The prevalence of these metabolites suggests that quetiapine urine drug testing would be more consistent with prescriptions when they are included in the analysis.
Data from Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;The purpose of this study was to measure genomic changes that emerge with enzalutamide treatment using analyses of whole-genome sequencing and RNA sequencing.&lt;/p&gt;Experimental Design:&lt;p&gt;One hundred and one tumors from men with metastatic castration-resistant prostate cancer (mCRPC) who had not been treated with enzalutamide (&lt;i&gt;n&lt;/i&gt; = 64) or who had enzalutamide-resistant mCRPC (&lt;i&gt;n&lt;/i&gt; = 37) underwent whole genome sequencing. Ninety-nine of these tumors also underwent RNA sequencing. We analyzed the genomes and transcriptomes of these mCRPC tumors.&lt;/p&gt;Results:&lt;p&gt;Copy number loss was more common than gain in enzalutamide-resistant tumors. Specially, we identified 124 protein-coding genes that were more commonly lost in enzalutamide-resistant samples. These 124 genes included eight putative tumor suppressors located at nine distinct genomic regions. We demonstrated that focal deletion of the 17q22 locus that includes &lt;i&gt;RNF43&lt;/i&gt; and &lt;i&gt;SRSF1&lt;/i&gt; was not present in any patient with enzalutamide-naïve mCRPC but was present in 16% (6/37) of patients with enzalutamide-resistant mCRPC. 17q22 loss was associated with lower &lt;i&gt;RNF43&lt;/i&gt; and &lt;i&gt;SRSF1&lt;/i&gt; expression and poor overall survival from time of biopsy [median overall survival of 19.3 months in 17q22 intact vs. 8.9 months in 17q22 loss, HR, 3.44 95% confidence interval (CI), 1.338–8.867, log-rank &lt;i&gt;P&lt;/i&gt; = 0.006]. Finally, 17q22 loss was linked with activation of several targetable factors, including CDK1/2, Akt, and PLK1, demonstrating the potential therapeutic relevance of 17q22 loss in mCRPC.&lt;/p&gt;Conclusions:&lt;p&gt;Copy number loss is common in enzalutamide-resistant tumors. Focal deletion of chromosome 17q22 defines a previously unappreciated molecular subset of enzalutamide-resistant mCRPC associated with poor clinical outcome.&lt;/p&gt;&lt;/div&gt;
Evaluation of Interface Adhesion Strength in Cu/(Ta–x% N, Ta/TaN)/SiO2/Si by Nanoscratch Test (2008)

The adhesion strength of Cu/(Ta–x% N, Ta/TaN)/SiO2/Si was investigated and the feasibility of the nanoscratch technique was evaluated. Because of the grain orientation dependence of critical load owing to elastic/plastic anisotropy, the interface adhesion measured in the mix-textured films of <111> and <100> showed a wide-range data spread to higher adhesion strength compared with the highly <111> textured films. The adhesive energy derived from the measured critical load by considering the residual stress and the effect of grain orientation by the aid of finite element method calculation showed a reasonable agreement with theoretical work of adhesion. It was revealed that the adhesion strength of Cu/Ta–x% N decreases with increasing nitrogen concentration. This tendency can be associated with increasing number of weak Cu–N bonding along the Cu/barrier interface.
Fixing Rule 702: The PCAST Report and Steps to Ensure the Reliability of Forensic Feature-Comparison Methods in the Criminal Courts (2018)

In response to PCAST’s recommendation, the Standing Advisory Committee on Evidence Rules convened a meeting on forensic expert testimony, Daubert, and Rule 702 on October 27, 2017, at Boston College Law School to inform itself about the issues.22 The meeting included presentations by twenty-six speakers (including myself) and discussion among the attendees. The purpose of this Article is to summarize aspects of the PCAST report relevant to its recommendation to the Standing Advisory Committee on Evidence Rules and to propose a path forward with respect to Rule 702.
Estimation of SI Engine Load Torque: Adaptive Kalman Filter vs. Luenberger Estimator (2004)

The SI engine load torque is key information for many engine and power train control systems. Since the torque is not measured in production vehicles, it needs to be estimated on-line. The paper presents design and analysis of second-order and third-order Luenberger load torque estimators. With the aim to reduce the estimator noise sensitivity without deteriorating its transient performance, an adaptive Kalman filter is proposed and compared with the Luenberger estimator. The adaptation mechanism is based on a load torque change detection algorithm. The estimators are examined by computer simulations and experiments.