gebhart/patrepeval huggingface dataset:
Opportunities for ionic liquids in recovery of biofuels (2001)

Room temperature ionic liquids have potential as extractants in recovery of butyl alcohol from fermentation broth; water solubility in ionic liquid and ionic liquid solubility in water are important factors affecting selectivity of butyl alcohol extraction from aqueous solutions.
Supplementary Figures 1 - 11 from Expression Profiling of Archival Tumors for Long-term Health Studies (2023)

&lt;p&gt;PDF file - 1787K, Supplemental Figure S1: Immunohistochemistry for selected proteins. Supplemental Figure S2: Pairwise scatterplots of technical variables for 1,003 DASL arrays from the NHS/HPFS study, including median value of Illumina control probes, sample age, RNA concentration, fraction of probes called present (p&lt;0.05), and Interquartile Range (IQR). Supplemental Figure S3: Spatial distribution of sample-independent positive control probes (CY3_HYB) across the 12 96-well plates of the NHS/HPFS experiment. Supplemental Figure S4: Spearman correlation of expression profiles of individual technical replicates to the median pseudochip decreases with Interquartile Range (IQR), particularly for samples with IQR less than 1. Supplemental Figure S5: CAT-boxplots for six covariates available in the NHS/HPFS study, showing reproducibility of ranked lists of differentially expressed between two independent samples by plotting fractional concordance of the top n genes in each list on the y-axis, against n on the x-axis. Supplemental Figure S6: Examples of two of the "best" (0.1% and 0.2% quantile) and "worst" (99.8% and 99.9% quantile) probes for reproducibility as assessed by Spearman correlation, Euclidian Distance, and Manhattan Distance. Supplemental Figure S7: Reproducibility of individual probe intensity measurements. For samples passing quality control in the BC/A experiment, Spearman correlation between technical replicates was calculated for each probe, as a function of four different measures of probe activity. Supplemental Figure S8: Analysis of probe reproducibility measured by Euclidian distance, and relationships between different probe filtering criteria. Supplemental Figure S9: t-statistics using samples passing strict QC and permissive QC for the molecular markers considered in Supplemental Table 1. Supplemental Figure S10: validation of MSI-associated mRNA transcripts previously reported from fresh-frozen tissues(24). Supplemental Figure S11: Distribution of presence calls (fraction of samples in which a probe is called present, p&lt;0.01) for all 24,526 probes on the DASL� assay, and for probes involved in validation of previously identified MSI-associated gene transcripts(24).&lt;/p&gt;
Sequentially Coated Wavy Nanowire Composite Transparent Electrode for Stretchable Solar Cells (2023)

Recent advances in fabricating stretchable and transparent electrodes have led to various techniques for establishing next-generation form-factor optoelectronic devices. Wavy Ag nanowire networks with large curvature radii are promising platforms as stretchable and transparent electrodes due to their high electrical conductivity and stretchability even at very high transparency. However, there are disadvantages such as intrinsic nonregular conductivity, large surface roughness, and nanowire oxidation in air. Here, we introduce electrically synergistic but mechanically independent composite electrodes by sequentially introducing conducting polymers and ionic liquids into the wavy Ag nanowire network to maintain the superior performance of the stretchable transparent electrode while ensuring overall conductivity, lower roughness, and long-term stability. In particular, plenty of ionic liquids can be incorporated into the uniformly coated conducting polymer so that the elastic modulus can be significantly lowered and sliding can occur at the nanowire interface, thereby obtaining the high mechanical stretchability of the composite electrode. Finally, as a result of applying the composite film as the stretchable transparent electrode of stretchable organic solar cells, the organic solar cell exhibits a high power conversion efficiency of 11.3% and 89% compared to the initial efficiency even at 20% tensile strain, demonstrating excellent stretching stability.
Identification and characterization of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates (2018)

Abstract Nitrogen-containing-bisphosphonates (N-BPs) are a class of drugs widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies have established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs. We observed that SLC37A3 forms a complex with ATRAID (all-trans retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. Our results elucidate the route by which N-BPs are delivered to their molecular target, addressing a key aspect of the mechanism of action of N-BPs that may have significant clinical relevance.
Significance of Aspect Ratio on Efficiency of Layered Double Hydroxide Flame Retardants (2012)

The effect of specific surface area and aspect ratio of different layered double hydroxides (LDHs) on flame retardant properties of PS/LDH nano-composites was systematically investigated. Carbonate LDH, with a Mg:Al molar ratio of 2:1, was synthesized by the urea hydrolysis method and external basal surfaces were selectively modified using a siderophilic ligand (3,4-dihydroxybenzo-phenone). The efficiency of this surface modification was investigated by studying the sedimentation kinetics in an organic solvent. PS/LDH nanocomposites were prepared by solution blending in a three roll mill. Cone calorimeter measurements showed little influence of specific surface areas but a pronounced influence of aspect ratio on flame retardancy. Optimizing aspect ratio yielded a significant reduction of the peak of heat release rate (PHRR) of 34 % at 5 wt% loading of LDH. A maximum reduction of PHRR of 51% could be achieved at a loading of 15wt%. Interestingly, at this loading an unusual increase of tign could be observed.
센서 측정기와 회로형 순환 유닛(GRU)을 이용한 실내 공기 품질 측정 및 추세 예측 시스템 (2017)

실내 공기 품질 측정은 측정 대상 공간의 대기 상태 유지, 외부 변인으로 인한 대기 이상 현상을 검출하려는 방법이다. 실내 공기 품질을 주기적으로 기록하면서 변인에 따른 공기 변화에 특정 패턴이 발생함을 관측할 수 있었으나, 파라미터를 설정하고 계수를 찾아 나가기엔 파라미터의 개수나 그 영향력을 추산하기 어렵고 결과가 시간에 의존적이라는 문제가 있다. 따라서 본 실험은 이것을 공식화하는 대신, 측정 주기마다 추이를 예측하는 관측치 중심의 기계 학습 모델을 개발하는 것을 목표로 한다. 본 논문은 실내 대기 품질을 주기적으로 전송 및 저장하는 측정기의 기록 데이터로 공기 품질 변화를 예측하는 모델을 설명하고 시계열 분석 모델을 구축한다.
Improving expression of recombinant human IGF‐1 using IGF‐1R knockout CHO cell lines (2015)

Chinese Hamster Ovary (CHO) cells are widely used for the large-scale production of recombinant biopharmaceuticals. However, attempts to express IGF-1 (a mutated human Insulin-like growth factor 1 Ea peptide (hIGF-1Ea mut)) in CHO cells resulted in poor cell growth and low productivity (0.1-0.2 g/L). Human IGF-1 variants negatively impacted CHO cell growth via the IGF-1 receptor (IGF-1R). Therefore knockout (KO) of the IGF-1R gene in two different CHO cell lines as well as knockdown (KD) of IGF-1R in one CHO cell line were performed. These cell line engineering approaches decreased significantly the hIGF-1 mediated cell growth inhibition and increased productivity of both KO CHO cell lines as well as of the KD CHO cell line. A productivity increase of 10-fold at pool level and sevenfold at clone level was achieved, resulting in a titer of 1.3 g/L. This data illustrate that cell line engineering approaches are powerful tools to improve the yields of recombinant proteins which are difficult to produce in CHO cells.
Creating volume-based virtual anatomy for bioengineering analysis (1996)

No abstract available.
Thrust Local Feed-Back Control for Realization of High Speed and Precise Motion in Water (2003)

水中において, スラスタが本体に与える推力を直接計測し, ローカルフィードバック制御する手法を提案する。本手法により, スラスタ駆動における流体が関係する複雑なダイナミクスを考慮することなく, 水中スラスタによる本体の高精度な制御が可能となる。
Untargeted Metabolite Profiling of Cerebrospinal Fluid Uncovers Biomarkers for Severity of Late Infantile Neuronal Ceroid Lipofuscinosis (CLN2, Batten Disease) (2018)

Abstract Late infantile neuronal ceroid lipofuscinosis ( CLN2 disease) is a rare lysosomal storage disorder caused by a monogenetic deficiency of tripeptidyl peptidase-1 (TPP1). Despite knowledge that lipofuscin is the hallmark disease product, the relevant TPP1 substrate and its role in neuronal physiology/pathology is unknown. We hypothesized that untargeted metabolite profiling of cerebrospinal fluid (CSF) could be used as an effective tool to identify disease-associated metabolic disruptions in CLN2 disease, offering the potential to identify biomarkers that inform on disease severity and progression. Accordingly, a mass spectrometry-based untargeted metabolite profiling approach was employed to differentiate CSF from normal vs. CLN2 deficient individuals. Of 1,433 metabolite features surveyed, 29 linearly correlated with currently employed disease severity scores. With tandem mass spectrometry 8 distinct metabolite identities were structurally confirmed based on retention time and fragmentation pattern matches, vs. standards. These putative CLN2 biomarkers include 7 acetylated species – all attenuated in CLN2 compared to controls. Because acetate is the major bioenergetic fuel for support of mitochondrial respiration, deficient acetylated species in CSF suggests a brain energy defect that may drive neurodegeneration. Targeted analysis of these metabolites in CSF of CLN2 patients offers a powerful new approach for monitoring CLN2 disease progression and response to therapy.
Supplemental Movie 3 from AXL Inhibition Sensitizes Mesenchymal Cancer Cells to Antimitotic Drugs (2023)

&lt;p&gt;Timelapse movie of HeLa cells treated with docetaxel (3nM).&lt;/p&gt;
Wide electrochemical window ionic salt for use in electropositive metal electrodeposition and solid state Li-ion batteries (2013)

A stable hydrophobic ionic crystalline solid comprised of the <italic>N</italic>-propyl-<italic>N</italic>-methylpiperidinium cation and hexafluorophosphate anion PP<sub>13</sub>PF<sub>6</sub> exhibits a remarkably wide electrochemical window of 7.2 V.
Site-specific Nitration of Apolipoprotein A-I at Tyrosine 166 Is Both Abundant within Human Atherosclerotic Plaque and Dysfunctional (2014)

We reported previously that apolipoprotein A-I (apoA-I) is oxidatively modified in the artery wall at tyrosine 166 (Tyr(166)), serving as a preferred site for post-translational modification through nitration. Recent studies, however, question the extent and functional importance of apoA-I Tyr(166) nitration based upon studies of HDL-like particles recovered from atherosclerotic lesions. We developed a monoclonal antibody (mAb 4G11.2) that recognizes, in both free and HDL-bound forms, apoA-I harboring a 3-nitrotyrosine at position 166 apoA-I (NO2-Tyr(166)-apoA-I) to investigate the presence, distribution, and function of this modified apoA-I form in atherosclerotic and normal artery wall. We also developed recombinant apoA-I with site-specific 3-nitrotyrosine incorporation only at position 166 using an evolved orthogonal nitro-Tyr-aminoacyl-tRNA synthetase/tRNACUA pair for functional studies. Studies with mAb 4G11.2 showed that NO2-Tyr(166)-apoA-I was easily detected in atherosclerotic human coronary arteries and accounted for ∼ 8% of total apoA-I within the artery wall but was nearly undetectable (>100-fold less) in normal coronary arteries. Buoyant density ultracentrifugation analyses showed that NO2-Tyr(166)-apoA-I existed as a lipid-poor lipoprotein with <3% recovered within the HDL-like fraction (d = 1.063-1.21). NO2-Tyr(166)-apoA-I in plasma showed a similar distribution. Recovery of NO2-Tyr(166)-apoA-I using immobilized mAb 4G11.2 showed an apoA-I form with 88.1 ± 8.5% reduction in lecithin-cholesterol acyltransferase activity, a finding corroborated using a recombinant apoA-I specifically designed to include the unnatural amino acid exclusively at position 166. Thus, site-specific nitration of apoA-I at Tyr(166) is an abundant modification within the artery wall that results in selective functional impairments. Plasma levels of this modified apoA-I form may provide insights into a pathophysiological process within the diseased artery wall.
Data from Prostate Cancer Risk Stratification via Nondestructive 3D Pathology with Deep Learning–Assisted Gland Analysis (2023)

&lt;div&gt;Abstract&lt;p&gt;Prostate cancer treatment planning is largely dependent upon examination of core-needle biopsies. The microscopic architecture of the prostate glands forms the basis for prognostic grading by pathologists. Interpretation of these convoluted three-dimensional (3D) glandular structures via visual inspection of a limited number of two-dimensional (2D) histology sections is often unreliable, which contributes to the under- and overtreatment of patients. To improve risk assessment and treatment decisions, we have developed a workflow for nondestructive 3D pathology and computational analysis of whole prostate biopsies labeled with a rapid and inexpensive fluorescent analogue of standard hematoxylin and eosin (H&amp;E) staining. This analysis is based on interpretable glandular features and is facilitated by the development of image translation–assisted segmentation in 3D (ITAS3D). ITAS3D is a generalizable deep learning–based strategy that enables tissue microstructures to be volumetrically segmented in an annotation-free and objective (biomarker-based) manner without requiring immunolabeling. As a preliminary demonstration of the translational value of a computational 3D versus a computational 2D pathology approach, we imaged 300 &lt;i&gt;ex vivo&lt;/i&gt; biopsies extracted from 50 archived radical prostatectomy specimens, of which, 118 biopsies contained cancer. The 3D glandular features in cancer biopsies were superior to corresponding 2D features for risk stratification of patients with low- to intermediate-risk prostate cancer based on their clinical biochemical recurrence outcomes. The results of this study support the use of computational 3D pathology for guiding the clinical management of prostate cancer.&lt;/p&gt;Significance:&lt;p&gt;An end-to-end pipeline for deep learning–assisted computational 3D histology analysis of whole prostate biopsies shows that nondestructive 3D pathology has the potential to enable superior prognostic stratification of patients with prostate cancer.&lt;/p&gt;&lt;/div&gt;
Facing more than moore, is magnetic microscopy the new Swiss knife for 3D defect localization in SiP? (2010)

So far, most of the defects at system level are assembly related. This trend obviously concerns Systems in Package, Stacked dies, Packages on Package devices, passive integration, integration of logic, power, wireless, analog, sensor and actuator in the same packaged device... All these Systems in Package defy our failure localization tools. For the first time, we have to face non transparent material, massive 3D structure with mandatory long working distance and need of relatively high spatial resolution. Magnetic microscopy has the ability do this as long as we are able to adapt its principle to the mandatory 3D sensitivity and resolution. We have developed a global 3D approach based on simulation in order to target μm resolution at long working distance.
The role of time constraints in the design of control for the jogger's problem (2002)

Control schemes in real-time sensor-based systems often operate under tight time constraints determined by the system sampling rate. One area where such constraints are especially severe is the sensor-based motion planning with dynamics in robotics. Though very important both theoretically and in practice, this problem has not been addressed so far. The typical sampling rates in such systems are 20 to 50 per second. This leaves only 20 to 50 msec for the whole cycle, including sensing, complex geometric (intelligence) analysis, calculations due to dynamics and control, and motion execution. As a first attempt to solve the problem, we show that the time constraints can be met by a combination of a simple model with a carefully chosen analytical solution of the dynamic equations. The resulting control scheme guarantees convergence and safety of motion, and blends well with kinematic path planning algorithms. Two such strategies are discussed, one using a simple heuristic and the other with local optimization.
Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues (2023)

Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.
Sensor devices comprising a metal-organic framework material and methods of making and using the same (2023)

Disclosed herein are embodiments of sensor devices comprising a sensing component able to determine the presence of, detect, and/or quantify detectable species in a variety of environments and applications. The sensing components disclosed herein can comprise MOF materials, plasmonic nanomaterials, or combinations thereof. In an exemplary embodiment, light guides can be coupled with the sensing components described herein to provide sensor devices capable of increased NIR detection sensitivity in determining the presence of detectable species, such as gases and volatile organic compounds. In another exemplary embodiment, optical properties of the plasmonic nanomaterials combined with MOF materials can be monitored directly to detect analyte species through their impact on external conditions surrounding the particle or as a result of charge transfer to and from the plasmonic material as a result of interactions with the plasmonic material and/or the MOF material.
Creation of a GUI for Zori, a Quantum Monte Carlo program, usingRappture (2007)

In their research laboratories, academic institutions produce some of the most advanced software for scientific applications.However, this software is usually developed only for local application in the research laboratory or for method development.In spite of having the latest advances in the particular field of science, such software often lacks adequate documentation and therefore is difficult to use by anyone other than the code developers.As such codes become more complex, so typically do the input files and command statements necessary to operate them.Many programs offer the flexibility of performing calculations based on different methods that have their own set of variables and options to be specified.Moreover, situations can arise in which certain options are incompatible with each other.For this reason, users outside the development group can be unaware of how the program runs in detail.The opportunity can be lost to make the software readily available outside of the laboratory of origin.This is a long-standing problem in scientific programming.
Tracking the evolution of structural resonances during the build phase of a wire-arc additively manufactured part (2021)

Acoustic resonance tracking is investigated for a wire arc additive manufacturing process as a possible real time in situ diagnostic during the build. A small 40kHz acoustic emission sensor was attached to one end of a 5 × 1.5 in. cylindrical 316 SS rod. A series of layers (weld beads) were programmed into the control software of the robot to build a thin bar upward off the end of the cylinder. A high-speed long-duration digitizer-recorder was used to capture the transient acoustic signals (100 Hz–70 kHz) during the build process. Typical build durations were on the order of 1–2 h. The transient data were analyzed using short time window FFTs, as a function of build parameters. The model and experiment share similar features, however there are some notable differences. In particular, the number of actual modes recorded in the experiment is less than predicted due to the sensors low in-plane sensitivity. The current results indicate that the evolving spectral response of a part during the build process has the potential to provide real time process monitoring information. The time-frequency analysis of the diffuse sound field in the part, reveals a unique spatial and temporal perspective of temperature, stress and geometric features.
Phase separation of polymerized mixed liposomes: analysis of release behavior of entrapped molecules with skeletonization (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhase separation of polymerized mixed liposomes: analysis of release behavior of entrapped molecules with skeletonizationShinji Takeoka, Hiromi Sakai, Hiroyuki Ohno, and Eishun TsuchidaCite this: Macromolecules 1991, 24, 6, 1279–1283Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/ma00006a011https://doi.org/10.1021/ma00006a011research-articleACS PublicationsRequest reuse permissionsArticle Views174Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Phase Shifts Induced by the Piezoelectric Transducers Attached to a Linearly Chirped Fiber Bragg Grating (2010)

A simple method enabling to generate a stable and controllable phase shift in a linearly chirped fiber Bragg grating (FBG) is theoretically and experimentally demonstrated, which is based on the utilization of the mini-size piezoelectric transducers (PZTs). The magnitude of the induced phase shift can easily be controlled by adjusting the voltage applied on the individual PZT. With this method, a narrow bandpass filter with 3-dB band width of 0.085 nm is obtained. Based on this kind of filter, an Erbium-doped fiber ring laser is also demonstrated, and both switchable and stable single-longitudinal-mode (SLM) laser emission is successfully realized.