gebhart/patrepeval huggingface dataset:
Supplementary Figures S1 - S10 from AR Expression in Breast Cancer CTCs Associates with Bone Metastases (2023)

&lt;p&gt;Supplementary Figure S1: RNA sequencing and pathway analysis of CTCs from Bone(+) versus Visceral(+) breast cancer patients. Supplementary Figure S2: Correlation between AR expression and AR signatures. Supplementary Figure S3: ER and PR expression in CTCs from Bone(+) versus Visceral(+) breast cancer patients. Supplementary Figure S4: AR antibody validation. Supplementary Figure S5: AR copy number assessment in breast cancer bone metastasis. Supplementary Figure S6: ER and PR expression in primary and metastatic breast cancer. Supplementary Figure S7: AR expression correlates with bone metastasis independently of ER status. Supplementary Figure S8: Enzalutamide treatment induces downregulation of a subset of AR-dependent genes in breast cancer cells. Supplementary Figure S9: AR shRNA validation. Supplementary Figure S10: AR inhibition does not alter primary tumor growth.&lt;/p&gt;
Magneto-Optical Kerr Effect probed using Ultrafast High-Order Harmonic EUV Light (2009)

We use tabletop high harmonics to detect the EUV transverse magneto-optical Kerr effect from a permalloy sample. We measure large asymmetries, up to 6%, around the M absorption edges of Fe (54eV) and Ni (67eV).
Learning reference governor for cycle-to-cycle combustion control with misfire avoidance in spark-ignition engines at high exhaust gas recirculation–diluted conditions (2020)

Cycle-to-cycle feedback control is employed to achieve optimal combustion phasing while maintaining high levels of exhaust gas recirculation by adjusting the spark advance and the exhaust gas recirculation valve position. The control development is based on a control-oriented model that captures the effects of throttle position, exhaust gas recirculation valve position, and spark timing on the combustion phasing. Under the assumption that in-cylinder pressure information is available, an adaptive extended Kalman filter approach is used to estimate the exhaust gas recirculation rate into the intake manifold based on combustion phasing measurements. The estimation algorithm is adaptive since the cycle-to-cycle combustion variability (output covariance) is not known a priori and changes with operating conditions. A linear quadratic regulator controller is designed to maintain optimal combustion phasing while maximizing exhaust gas recirculation levels during load transients coming from throttle tip-in and tip-out commands from the driver. During throttle tip-outs, however, a combination of a high exhaust gas recirculation rate and an overly advanced spark, product of the dynamic response of the system, generates a sequence of misfire events. In this work, an explicit reference governor is used as an add-on scheme to the closed-loop system in order to avoid the violation of the misfire limit. The reference governor is enhanced with model-free learning which enables it to avoid misfires after a learning phase. Experimental results are reported which illustrate the potential of the proposed control strategy for achieving an optimal combustion process during highly diluted conditions for improving fuel efficiency.
Microfluidic Cell Retention Device for Perfusion of Mammalian Suspension Culture (2017)

Continuous production of biologics, a growing trend in the biopharmaceutical industry, requires a reliable and efficient cell retention device that also maintains cell viability. Current filtration methods, such as tangential flow filtration using hollow-fiber membranes, suffer from membrane fouling, leading to significant reliability and productivity issues such as low cell viability, product retention, and an increased contamination risk associated with filter replacement. We introduce a novel cell retention device based on inertial sorting for perfusion culture of suspended mammalian cells. The device was characterized in terms of cell retention capacity, biocompatibility, scalability, and long-term reliability. This technology was demonstrated using a high concentration (>20 million cells/mL) perfusion culture of an IgG<sub>1</sub>-producing Chinese hamster ovary (CHO) cell line for 18-25 days. The device demonstrated reliable and clog-free cell retention, high IgG<sub>1</sub> recovery (>99%) and cell viability (>97%). Lab-scale perfusion cultures (350 mL) were used to demonstrate the technology, which can be scaled-out with parallel devices to enable larger scale operation. The new cell retention device is thus ideal for rapid perfusion process development in a biomanufacturing workflow.
Janus-faced role of water in defining nanostructure of choline chloride/glycerol deep eutectic solvent (2018)

Deep eutectic solvents (DESs) have emerged as a set of intrinsically "designer solvents" for many bio-applications such as DNA nanotechnology and biocatalysis. However, the high viscosity of DESs tends to prevent bioactive components from being incorporated into the solvent. Although dilution with water may effectively reduce the viscosity of DES, the effect of water on its cooperative hydrogen-bonding network has not been evaluated systematically. This study conducted a series of molecular dynamics simulations on the DES made of choline chloride and glycerol at different hydration levels. We discovered a Janus-faced role of water in defining the interactive network between choline chloride and glycerol. Chloride played a critical role in bridging choline and glycerol in the anhydrous mixture. But the addition of water results in the decrease in the number of choline-chloride-glycerol supramolecular complexes and the number of hydrogen bonds between choline and glycerol, demonstrating the de-structuring effect of water. Interestingly, we also found that water could link choline to glycerol in place of chloride. The structuring role of water in bridging choline and glycerol reached its maximum in the presence of 35.8 wt% water. The findings in this study will provide valuable guidance to determine the optimal water content that can sufficiently "liquidize" DESs and meanwhile maintain the majority of the eutectic stoichiometry in the DESs, paving the way for tapping the full potential of DESs as the intrinsically "designer solvents".
Effects of Atrazine in Fish, Amphibians, and Reptiles: An Analysis Based on Quantitative Weight of Evidence (2014)

A quantitative weight of evidence (WoE) approach was developed to evaluate studies used for regulatory purposes, as well as those in the open literature, that report the effects of the herbicide atrazine on fish, amphibians, and reptiles. The methodology for WoE analysis incorporated a detailed assessment of the relevance of the responses observed to apical endpoints directly related to survival, growth, development, and reproduction, as well as the strength and appropriateness of the experimental methods employed. Numerical scores were assigned for strength and relevance. The means of the scores for relevance and strength were then used to summarize and weigh the evidence for atrazine contributing to ecologically significant responses in the organisms of interest. The summary was presented graphically in a two-dimensional graph which showed the distributions of all the reports for a response. Over 1290 individual responses from studies in 31 species of fish, 32 amphibians, and 8 reptiles were evaluated. Overall, the WoE showed that atrazine might affect biomarker-type responses, such as expression of genes and/or associated proteins, concentrations of hormones, and biochemical processes (e.g. induction of detoxification responses), at concentrations sometimes found in the environment. However, these effects were not translated to adverse outcomes in terms of apical endpoints. The WoE approach provided a quantitative, transparent, reproducible, and robust framework that can be used to assist the decision-making process when assessing environmental chemicals. In addition, the process allowed easy identification of uncertainty and inconsistency in observations, and thus clearly identified areas where future investigations can be best directed.
A randomized phase II study of OGX-427 plus prednisone (P) versus P alone in patients (pts) with metastatic castration resistant prostate cancer (CRPC). (2012)

4514 Background: Heat Shock Protein 27 (Hsp27) is a multi-functional chaperone protein that regulates cell signaling and survival pathways implicated in cancer progression. In prostate cancer models, Hsp27 complexes with androgen receptor (AR) and enhances transactivation of AR-regulated genes. OGX-427 is a 2nd generation antisense oligonucleotide that inhibits Hsp27 expression with in vitro and in vivo efficacy and was well tolerated with single agent activity in phase I studies. Methods: Chemotherapy-naïve pts with no/minimal symptoms were randomized to receive OGX-427 600 mg IV x 3 loading doses then 1000 mg IV weekly with P 5 mg PO BID or P only. Primary endpoint was the proportion of pts progression free (PPF) at 12 weeks (PCWG2 criteria). A 2-stage MinMax design (H 0 = 5%, H A &gt;20%, α=0.1, β=0.1) with 32 pts/arm provides 70% power to detect the difference at 0.10 1-sided significance. Secondary endpoints include PSA decline, measurable disease response, and circulating tumour cell (CTC) enumeration. Results: 38 pts have been enrolled; 1st stage of accrual completed with 2nd stage accruing. In the 1st 32 pts randomized (17 to OGX-427+P, 15 to P), baseline median age was 71 years (53-89), ECOG PS 0 or 1 in 66% and 34% of pts, median PSA 66 (6-606), metastases in bone/lymph nodes/liver or lung was 75/56/9%, 31% had prior P treatment, and 93% had ≥5 CTC/7.5 ml. Predominantly grade 1/2 infusion reactions (chills, diarrhea, flushing, nausea, vomiting) occurred in 47% of pts receiving OGX-427+P. One pt on OGX-427+P developed hemolytic uremic syndrome. A PSA decline of ≥50% occurred in 41% of pts on OGX-427+P, and 20% of pts treated with P. A measurable disease partial response was seen in 3/8 (38%) evaluable pts on OGX-427+P and 0/9 pts on P. CTC conversion from ≥5 to &lt;5/7.5 ml occurred in 50% of pts on OGX-427+P and 31% treated with P. Thus far, in 26 evaluable pts the PPF at 12 weeks was 71% (95% CI: 42-92) in OGX-427+P treated pts and 33% (95% CI: 10-65) in pts on P. Conclusions: These data provide clinical evidence for the role of Hsp27 as a therapeutic target in prostate cancer and support continued evaluation of OGX-427 for pts with CRPC. Funded by a grant from the Terry Fox Research Institute.
NOMA Aided Narrowband IoT for Machine Type Communications With User Clustering (2019)

To support machine type communications (MTCs) in next generation mobile networks, Narrowband-Internet of Things (NB-IoT) has been released by the third generation partnership project (3GPP) as a promising solution to provide extended coverage and low energy consumption for low cost MTC devices. However, the existing orthogonal multiple access (OMA) scheme in NB-IoT cannot provide connectivity for a massive number of MTC devices. In parallel with the development of NB-IoT and non-OMA (NOMA), introduced for the fifth generation wireless networks, is deemed to significantly improve the network capacity by providing massive connectivity through sharing the same spectral resources. To leverage NOMA in the context of NB-IoT, we propose a power domain NOMA scheme with user clustering for an NB-IoT system. In particular, the MTC devices are assigned to different ranks within the NOMA clusters where they transmit over the same frequency resources. Then, we formulate an optimization problem to maximize the total throughput of the network by optimizing the resource allocation of MTC devices and NOMA clustering while satisfying the transmission power and quality of service requirements. We prove the NP-hardness of the proposed optimization problem. We further design an efficient heuristic algorithm to solve the proposed optimization problem by jointly optimizing NOMA clustering and resource allocation of MTC devices. Furthermore, we prove that the reduced optimization problem of power control is a convex optimization task. Simulation results are presented to demonstrate the efficiency of the proposed scheme.
Corrigendum: An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes (2018)

[This corrects the article DOI: 10.3389/fmicb.2017.00386.].
S162013 A study on sound-generating mechanism of a paper : Improvement of collision noise of a paper (2011)

Copy machines are becoming much faster and are demanded to reduce noise at the sometime. The proportion of collision noise of a paper becomes larger as the copy machines become faster. On the other hand, the sound emission of a paper affects sound quality. The purpose of this study is to achieve a pleasant sound by changing the quality of the sound of radiated sound of the paper without increasing the noise level. Experiments were conducted by experimental equipment based on paper handling machine. The collision noise were generated by giving an impact force on one end of the paper. Resonant frequency of the paper by edge emission and by surface emission were nearly identical. Also, the resonant frequency of a paper appeared mainly in low frequency band. When controlled wave that has passed 100" 500Hz band pass filter was applied on collision noise of the paper, the low frequency region was emphasized. This changed the quality of collision noise of the paper, and a pleasant sound was aand achieved without increasing the noise level.
Subcritical Crack Growth in Lead Zirconate Titanate (2004)

Subcritical crack growth in terms of velocity–stress intensity factor ( v – K ) curves in lead zirconate titanate (PZT) were experimentally characterized on poled and unpoled compact tension specimens. The poled specimens were tested under open‐ and short‐circuit electrical boundary conditions, which resulted in an increase in fracture toughness by 0.2 MPa·m 1/2 for the accessible velocity range ( v = 10 −9 to 10 −4 m/s) in the open‐circuit case. Subcritical crack growth of unpoled specimens was obtained under ambient (relative humidity = 35%) and dry (relative humidity ∼ 0.02%) conditions over a regime in stress intensity factor of 0.5 MPa·m 1/2 .
Supplementary Figures from An Expression Signature as an Aid to the Histologic Classification of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Sup. fig. 1, signature optimization; sup. fig. 2, Score plot of both signatures; sup. fig. 3, score box plots; sup. fig. 4, association between score and tumor differentiation; sup. fig. 5, association of score with survival; sup. fig. 6, HTG EdgeSeq assay on 25 samples&lt;/p&gt;
Commutativity-based concurrency control for abstract data types (1988)

Two novel concurrency algorithms for abstract data types are presented that ensure serializability of transactions. It is proved that both algorithms ensure a local atomicity property called dynamic atomicity. The algorithms are quite general, permitting operations to be both partial and nondeterministic. The results returned by operations can be used in determining conflicts, thus allowing higher levels of concurrency than otherwise possible. The descriptions and proofs encompass recovery as well as concurrency control. The two algorithms use different recovery methods: one uses intentions lists, and the other uses undo logs. It is shown that conflict relations that work with one recovery method do not necessarily work with the other. A general correctness condition that must be satisfied by the combination of a recovery method and a conflict relation is identified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pregnane-Type Brassinosteroids with a Four-Carbon Ester Functionality in Position 20 (1996)

Analogues of brassinolide and castasterone, containing an ester functionality with four carbon atoms in the position 20 of the pregnane skeleton, have been prepared. In the bean second internode assay the most effective compounds were (20 R )-2α,3α,20-trihydroxy-5α-pregnan-6-one 20-isobutyrate ( 6d ) and (20 R )-2α,3α,20-trihydroxy-B-homo-7-oxa-5α-pregnan-6-one 20-isobutyrate ( 7d ). On the other hand, (20 R )-2α,3α,20-trihydroxy-B-homo-6-oxa-5α-pregnan-7-one 20-heptafluorobutyrate ( 8 ) was the first compound with the retarding effect in the same test.
Age-dependent saccadic models for predicting eye movements (2017)

How people look at visual information reveals fundamental information about themselves, their interests and their state of mind. While previous visual attention models output static 2-dimensional saliency maps, saccadic models predict not only what observers look at but also how they move their eyes to explore the scene. Here we demonstrate that saccadic models are a flexible framework that can be tailored to emulate the gaze patterns from childhood to adulthood. The proposed age-dependent saccadic model not only outputs human-like, i.e. age-specific visual scanpath, but also significantly outperforms other state-of-the-art saliency models.
Supplementary Figure 3 from miR-31 Is a Broad Regulator of β1-Integrin Expression and Function in Cancer Cells (2023)

&lt;p&gt;PDF file - 19K&lt;/p&gt;
Reduction of metal adducts in oligonucleotide mass spectra in ion‐pair reversed‐phase chromatography/mass spectrometry analysis (2016)

Implementation of a short low pH reconditioning step was observed to effectively displace trace metal salts non-specifically adsorbed to surfaces in the fluidic path and was able to maintain an average MS spectral abundance ≥94% with a high degree of repeatability (relative standard deviation (R.S.D.) 0.8%) over an extended time study. The proposed method offers the ability to rapidly regenerate adsorption sites with minimal impact on productivity while retaining assay sensitivity afforded by MS detection with reduced adduct formation. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.
Abstract 2934: Novel approach for treating neural crest derived tumors: Selective inhibition of ganglioside biosynthesis with small molecules (2011)

Abstract Neural crest derived tumors express high levels of a unique class of lipid linked glycan known as gangliosides. Gangliosides are involved in growth factor signaling by regulating complexes in lipid rafts. Genetic studies show that through aberrant expression of gangliosides, these tumors acquire aggressive growth properties. Prior to this research, the only ganglioside inhibitors identified were non-specific and broadly blocked virtually all glycolipid classes. These non-specific glycolipid inhibitors demonstrated anti-cancer activity in animal models of neural crest tumors. However, due to substantial off-target dose-limiting toxicity from lack of specificity for the ganglioside sub-class, they effectively cannot be used in humans for cancer treatment. Selective inhibition of gangliosides without affecting other glycan classes could potentially avoid these problems and provide an effective treatment for neural crest and other ganglioside-dependent tumors. To identify the first known selective inhibitors of gangliosides, we developed a novel molecular screening strategy for identifying selective small-molecule ganglioside inhibitors. This platform identified the first drug-like selective inhibitors of gangliosides. ZP10395, a lead compound, selectively and dose-dependently reduces gangliosides in multiple tumor cell lines and is 10-15 fold more potent than the existing non-specific inhibitors. Importantly, it does not inhibit other glycolipid classes associated with dose-limiting toxicity. Administering ZP10395 to a mouse xenograph melanoma model significantly reduced ganglioside production and slowed tumor growth in the presence of a reduced T-cell response. These results demonstrate the potential utility of specific ganglioside inhibitors for treating ganglioside dependent tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2934. doi:10.1158/1538-7445.AM2011-2934
Feasibility and safety of mannitol challenge in pre-school children using forced oscillations (2012)

Background: The mannitol dry powder challenge is used to identify exercise induced bronchoconstriction (EIB) in adults and school-age children. The forced oscillation technique (FOT) is suitable for assessing lung function in pre-school children and can be combined with inhaled challenge testing in this age group.

Aims: This study aimed to assess the safety and the feasibility of a mannitol challenge using FOT in young children with asthma and in healthy controls.

Methods: Healthy children and children with exercise induced symptoms (EIS group) aged 3-7 years were recruited. A mannitol challenge (Aridol, Pharmaxis, Australia) was performed. A positive response to mannitol was defined as wheeze on auscultation, persistent cough, SpO2 50% from control. The mannitol challenge was considered successful if the child completed the challenge to the final dose or a positive response was noted.

Results: To date, 6 healthy and 10 EIS children have been studied. 14 children successfully completed the mannitol challenge with no adverse events. Two healthy children aged 3 years did not complete the test due to lack of cooperation. Three children with reported EIS responded to the challenge with symptoms, and three children responded by an increase in the Rrs8 by >50% from the control measurement.

Conclusion: These preliminary results suggest that a mannitol challenge test is feasible in young children and can be performed safely.

Funded by: ANZSRS Research Grant, Asthma Foundation WA.
Array-Based Electrical Detection of DNA with Nanoparticle Probes* (2020)

A DNA array detection method is reported in which the binding of oligonucleotides functionalized with gold nanoparticles leads to conductivity changes associated with target-probe binding events. A major challenge in the area of DNA detection is the development of methods that do not rely on polymerase chain reaction or comparable target-amplification systems that require additional instrumentation and reagents that are not ideal for point-of-care or field use. In principle, capacitance or conductivity measurements can be made to determine the number of particles and, therefore, target molecules that fill the gap. In the absence of a stringency wash, the gap resistances decrease with increasing exposure to the silver enhancer solution for all complementary and non-complementary strands. A conventional way of increasing target selectivity is to wash a DNA chip array with a buffer solution at a temperature that results in the dehybridization of DNA duplexes formed from non-complementary strands.
Corrigendum (1993)

D. Zeng, M. J. Hampden-Smith and L. Wang, J. Mater. Chem., 1993, 3, 777 DOI: 10.1039/JM9930300777