gebhart/patrepeval huggingface dataset:
Star-Shaped Poly(tetrahydrofuran) with Reactive End Groups:  Design, MALDI-TOF Study, and Solution Behavior (2005)

Star-shaped poly(tetrahydrofuran) (PTHF) with up to six allyl end groups was prepared by living cationic ring-opening polymerization. A functional initiation system, using allyl alcohol and trifluoromethanesulfonic anhydride, was used, followed by end-capping of the living polymer chains with the multifunctional termination agent tris(2-aminoethyl)amine. In this way, star-shaped PTHF with allyl end groups could be synthesized, with varying molecular weight (6000−20 000 g·mol-1) and number of arms (three to six). Subsequently, the terminal allyl functions were quantitatively transformed into hydroxy groups using a hydroboration procedure. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis, NMR, and size exclusion chromatography confirmed the controlled synthesis of these reactive star-shaped structures. MALDI-TOF was successfully used to determine the absolute molecular weight and purity of star-shaped polymers. They were further characterized by viscosimetry measurements, and their properties were compared to their linear analogues. For the same molecular weight, the stars had a strong reduced viscosity in solution.
Synthesis of (R) and (S) 14C-labelled ethyl nipecotate, for preparation of GABA uptake ligands (1997)

14C-labelled (R)- and (S)-ethyl 3-[carboxyl-14C]piperidinecarboxylate were synthesised in 3 steps, including a chiral HPLC separation, starting from 3-[carboxyl-14C]pyridine-carboxylate. The overall radiochemical yield of the labelled (R)- and (S)-enantiomers were 67% and 61%. The radiochemical purities were higher than 98% with specific radioactivities of 48 mCi/mmol. © 1997 John Wiley & Sons, Ltd.
Analysis of an adjustable field permanent magnet solenoid (2017)

A feasibility study has been performed on an adjustable-field permanent magnet (PM) solenoid concept in an effort to reduce the dependence that linear induction accelerators have on large direct current power supplies and associated cooling systems. The concept relies on the ability to reorient sections of the PMs and thus redirect their magnetization vector to either add to or subtract from the on-axis magnetic field. This study concentrated on the focal strengths and emittance growths for two different designs, both with 19 cm bore diameters extending 53 cm in length. The first design is expected to produce peak magnetic fields ranging from 260 to 900 G (0.026 to 0.09 T) while the second design is expected to produce peak magnetic fields ranging from 580 to 2100 G (0.058 to 0.21 T). Finally, although the PM configuration generates a variable magnetic field and the torques acting on PMs within the assembly appear manageable, the emittance growth is larger than that of a DC solenoid.
Partial inhibition of activin receptor-like kinase 4 attenuates pressure overload-induced cardiac fibrosis and improves cardiac function (2016)

Our results demonstrate that ALK4 haploinsufficiency ameliorates cardiac fibrosis and dysfunction in a mouse pressure-overload model associated with inhibition of cardiac fibroblast activation and cardiomyocyte apoptosis through the suppression of Smad2/3 activity, and suggest that ALK4 is a novel therapeutic target in treating pressure overload-induced cardiac remodeling and heart failure.
Proteomic Characterization of the Dynamics of Ischemic Stroke in Mice (2021)

Novel therapies and biomarkers are needed for the treatment of acute ischemic stroke (AIS). This study aimed to provide comprehensive insights into the dynamic proteome changes and underlying molecular mechanisms post-ischemic stroke. TMT-coupled proteomic analysis was conducted on mouse brain cortex tissue from five time points up to 4 weeks poststroke in the distal hypoxic-middle cerebral artery occlusion (DH-MCAO) model. We found that nearly half of the detected proteome was altered following stroke, but only ∼8.6% of the changes were at relatively large scales. Clustering on the changed proteome defined four distinct expression patterns characterized by temporal and quantitative changes in innate and adaptive immune response pathways and cytoskeletal and neuronal remodeling. Further analysis on a subset of 309 "top hits", which temporally responded to stroke with relatively large and sustained changes, revealed that they were mostly secreted proteins, highly correlated to different cortical cytokines, and thereby potential pharmacodynamic biomarker candidates for inflammation-targeting therapies. Closer examination of the top enriched neurophysiologic pathways identified 57 proteins potentially associated with poststroke recovery. Altogether, our study generated a rich dataset with candidate proteins worthy of further validation as biomarkers and/or therapeutic targets for stroke. The proteomics data are available in the PRIDE Archive with identifier PXD025077.
Efficacy of opioid analgesics and effect on functional status of pain caused by radiation-induced mucositis among patients with head and neck cancer (2008)

6019 Background: Radiation (RT) to the oral cavity (OC), oropharynx (OP), larynx (L), or hypopharynx (HP) causes severe and debilitating mucositis in most patients (pts), particularly when chemotherapy (CT) is administered concomitantly. There are no available agents to prevent mucositis in pts with these cancers, thus, the standard of care is pain control, using opioids when pain is severe. We prospectively studied the risk and severity of mucositis during RT, its impact on daily activities, and analgesic use. Methods: The Triad Burden of Illness study is an international, 41-center, prospective study of the risks for and outcomes of RT- and CT-induced mucositis. At baseline and daily during RT, pts with L/HP or OC/OP cancers completed a previously validated survey describing severity of mouth and throat soreness (MTS) measured from 0 (“no soreness”) to 4 (“extreme soreness”), its interference with drinking, eating, talking, and sleeping measured from 0 (“not limited”) to 4 (“unable to do”), and use of analgesics. Results: To date, 191 evaluable pts have completed RT; 77% were males, and 88% were non-Hispanic whites. All received single daily fractions of RT; 60% had concomitant CT, 57% had intensity modulated RT, and 34% had concomitant boost. Most pts (98%) developed mucositis; 82% reported severe pain (MTS 3–4). Despite regular analgesic use (> 4 days per week) by 83%, and opioid use by 65%, mean MTS remained >2 from weeks 5 - 7 of RT. Use of analgesics, opioids and limitations to daily activities were significantly associated with mucositis severity. Conclusions: The pain caused by radiation-induced mucositis is severe, debilitating and poorly controlled by analgesics among pts with head and neck cancers. Preventive strategies are needed. Maximum MTS 0–2 N=34 % of total (CI) Maximum MTS 3–4 N=157 % of total (CI) P value Regular analgesic use 65 (49-81) 87 (82-92) 0.001 Opioid use 44 (27-62) 70 (62-77) 0.004 Activity limited a lot or unable to do Drinking 6 (1-20) 92 (87-96) <0.001 Eating 21 (9-38) 97 (93-99) <0.001 Talking 24 (11-41) 83 (77-89) <0.001 Sleeping 21 (9-38) 71 (63-78) <0.001 Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Amgen
Experiences with commonality control procedures to develop clinical instrument system (2014)

This paper reports our experience with software development based on the Software Product Line (SPL) approach employed for Clinical Instrument Integration Management Software (CIIMS). CIIMS is the system software which systemizes heterogeneous clinical instruments. These instruments require their particular management so that various parts of CIIMS are forced to be changed. This makes it difficult to create development plans to connect new instruments to CIIMS. In this paper we summarize a new estimate method called the Architecture Domain Matrix (ADM) method which effectively solved this problem in our experience. In ADM each architectural element is further decomposed into clinical operation flow elements and core assets of software are extracted from these elements. This method estimates the CIIMS commonality with precision and finally enables to successfully connect new instruments. In addition this method provides a Work Breakdown Structure (WBS) and supports development team building. WBS is generated by collecting all the changes for each operational flow element. A development team suitable for change is organized by taking into consideration all the changes for each architecture element. We integrated three different instruments into CIIMS in 18 months after applying this method to a real project and achieved 2.5 times greater productivity with the embedded software than that with our previous non-SPL process.
Observation of conduction electron spin resonance in boron doped diamond (2013)

We observe the electron spin resonance of conduction electrons in boron doped (6400 ppm) superconducting diamond (Tc =3.8 K). We clearly identify the benchmarks of conduction electron spin resonance (CESR): the nearly temperature independent ESR signal intensity and its magnitude which is in good agreement with that expected from the density of states through the Pauli spin-susceptibility. The temperature dependent CESR linewidth weakly increases with increasing temperature which can be understood in the framework of the Elliott-Yafet theory of spin-relaxation. An anomalous and yet unexplained relation is observed between the g-factor, CESR linewidth, and the resistivity using the empirical Elliott-Yafet relation.
CajunBot: Architecture and algorithms (2006)

Abstract CajunBot, an autonomous ground vehicle and a finalist in the 2005 DARPA Grand Challenge, is built on the chassis of MAX IV, a six‐wheeled all‐terrain vehicle (ATV). Transformation of the ATV to an autonomous ground vehicle required adding drive‐by‐wire control, lidar sensors, an inertial navigation system (INS), and a computing system. Significant innovations in the core computational algorithms include an obstacle detection algorithm that takes advantage of shocks and bumps to improve visibility; a path planning algorithm that takes into account the vehicle's maneuverability limits to generate paths that are navigable at high speed; efficient data structures and algorithms that require just a single Intel Pentium 4 HT 3.2 GHz machine to handle all computations and a middleware layer that transparently distributes the computation to multiple machines, if desired. In addition, CajunBot also features support technologies, such as a simulator, playback of logged data, and live visualization on off‐board computers to aid in development, testing, and debugging. © 2006 Wiley Periodicals, Inc.
Data from Pancreatic Cancer Risk and ABO Blood Group Alleles: Results from the Pancreatic Cancer Cohort Consortium (2023)

&lt;div&gt;Abstract&lt;p&gt;A recent genome-wide association study (PanScan) identified significant associations at the ABO gene locus with risk of pancreatic cancer, but the influence of specific ABO genotypes remains unknown. We determined ABO genotypes (OO, AO, AA, AB, BO, and BB) in 1,534 cases and 1,583 controls from 12 prospective cohorts in PanScan, grouping participants by genotype-derived serologic blood type (O, A, AB, and B). Adjusted odds ratios (ORs) for pancreatic cancer by ABO alleles were calculated using logistic regression. Compared with blood type O, the ORs for pancreatic cancer in subjects with types A, AB, and B were 1.38 [95% confidence interval (95% CI), 1.18–1.62], 1.47 (95% CI, 1.07–2.02), and 1.53 (95% CI, 1.21–1.92), respectively. The incidence rates for blood types O, A, AB, and B were 28.9, 39.9, 41.8, and 44.5 cases per 100,000 subjects per year. An increase in risk was noted with the addition of each non-O allele. Compared with OO genotype, subjects with AO and AA genotype had ORs of 1.33 (95% CI, 1.13–1.58) and 1.61 (95% CI, 1.22–2.18), whereas subjects with BO and BB genotypes had ORs of 1.45 (95% CI, 1.14–1.85) and 2.42 (1.28–4.57). The population attributable fraction for non-O blood type was 19.5%. In a joint model with smoking, current smokers with non-O blood type had an adjusted OR of 2.68 (95% CI, 2.03–3.54) compared with nonsmokers of blood type O. We concluded that ABO genotypes were significantly associated with pancreatic cancer risk. Cancer Res; 70(3); 1015–23&lt;/p&gt;&lt;/div&gt;
Withdrawal syndrome after continuous infusion of clonidine in the normotensive rat (1981)

The effects on heart rate and arterial pressure of continuous subcutaneous infusion of clonidine (500 microgram kg-1 day-1) via an ALZET miniosmopump and sudden termination of this treatment were studied in conscious normotensive rats. No consistent decreases of heart rate and blood pressure were observed during the clonidine infusion. Within a few hours following removal of the minipumps, a pronounced and long-lasting tachycardia developed. Mean arterial pressure did not exceed control level consistently, but transient blood pressure 'upswings' were observed. The withdrawal phenomena were accompanied by a small, significant rise in plasma noradrenaline content. During the clonidine-infusion period piloerection and sedation were prominent. The present study indicates, that the occurrence of the withdrawal phenomena following cessation of clonidine treatment is not dependent upon a decrease of blood pressure and heart rate preceding clonidine withdrawal. Furthermore, the model presented may be suitable for the study of withdrawal phenomena of other anti-hypertensive drugs.
Diverse Fates of β‐Silyl Radical under Manganese Catalysis: Hydrosilylation and Dehydrogenative Silylation of Alkenes (2018)

Abstract Manganese‐catalyzed hydrosilylation of alkenes has been underdeveloped for a long time. Herein, we describe a general, chemo‐ and regio‐ selective hydrosilylation of alkenes by using the Mn(CO) 5 Br catalyst with ample substrate scopes. Meanwhile, dehydrogenative silylation of aryl olefins can be selectively achieved upon the catalysis of dinuclear Mn 2 (CO) 10 . Mechanistic experiments revealed diverse fates of the common intermediate β‐silyl radical, namely, hydrogen atom transfer (HAT) for the hydrosilylation and organometallic β‐H elimination for the dehydrogenative silylation of olefins.
Multi-Objective Optimization Design of a Stator Coreless Multidisc Axial Flux Permanent Magnet Motor (2022)

The stator coreless axial flux permanent magnet (AFPM) motor with a compact structure, low torque ripple, and high efficiency is particularly suitable as a motor for electric propulsion systems. However, it still requires great effort to design an AFPM motor with higher torque density and lower torque ripple. In this paper, a stator coreless multidisc AFPM (SCM-AFPM) motor with a three-rotor and two-stator topology is proposed. To reduce rotor mass and increase torque density, the proposed SCM-AFPM motor adopts the hybrid permanent magnets (PMs) array with Halbach PMs in the two-terminal rotor and the conventional PMs array in the middle rotor. In addition, a multi-objective optimization model combining response surface method (RSM) and genetic algorithm (GA) is proposed and applied to the proposed SCM-AFPM motor. With the help of the three-dimensional finite-element analysis (3-D FEA), it is found that the torque ripple of the optimized SCM-AFPM motor is 4.73%, while it is 6.21% for the initial motor. Its torque ripple is reduced by 23.8%. Therefore, the proposed multi-objective optimization design method can quickly and reliably obtain the optimal design of the SCM-AFPM motor.
Synthesis of High‐Quality Diesel with Furfural and 2‐Methylfuran from Hemicellulose (2012)

Hydroxyalkylation-alkylation (HAA) coupled with hydrodeoxygenation is a promising route for the synthesis of renewable high-quality diesel or jet fuel. In this work, a series of solid-acid catalysts were firstly used for HAA between lignocellulose-derived furan and carbonyl compounds. Among the investigated catalysts, Nafion-212 resin demonstrated the highest activity and stability. Owing to the high activity of the reactants and the advantage in industrial integration, the HAA of 2-methylfuran (2-MF) and furfural can be considered as a prospective route in future applications. Catalyst loading, reaction temperature, and time had evident effects on the HAA of 2-MF and furfural over Nafion-212 resin. Finally, the HAA product of 2-MF and furfural was hydrogenated over a Pd/C catalyst and hydrodeoxygenated over Pt-loaded solid-acid catalysts. Pt/zirconium phosphate (Pt/ZrP) was found to be the best catalyst for hydrodeoxygenation. Over the 4 % Pt/ZrP catalyst, a 94 % carbon yield of diesel and 75 % carbon yield of C15 hydrocarbons (with 6-butylundecane as the major component) was achieved.
Korea’s metal resources recycling research project – valuable recycling (2018)

South Korea imports 99% of its mineral metal resources, so it is important to recover valuable metals from metal-containing waste for sustainable domestic industry development. The Korean government launched a 10-year recycling research project, ‘Valuable Recycling’, in May 2011 with $180 million funding ($150 million from the government). The objectives of the project were to develop highly efficient technologies that improve the resource recycling ratio and quality of life, and meet international environmental regulations for enhancing the competitiveness of domestic industries. The project includes 26 sub-projects classified into four categories: electrical & electronics, automotive, metals & inorganics, and organics. The main research achievements and recycling processes are presented in this article.
A Screening Pipeline for Antiparasitic Agents Targeting Cryptosporidium Inosine Monophosphate Dehydrogenase (2010)

We have used these assays to evaluate C. parvum IMPDH inhibitors emerging from our ongoing medicinal chemistry effort and have identified a subset of 1,2,3-triazole ethers that exhibit excellent in vivo selectivity in the T. gondii model and improved anti-cryptosporidial activity.
Evaluation of Accuracy in Ankle Center Location for Tibial Mechanical Axis Identification (2004)

Many surgical computer-assisted systems use mechanical axis identification as a reference for their computations. The goal of this study was to compare three methods to determine the location of the distal point of the tibial mechanical axis, based on percutaneous digitization of definite anatomical landmarks. In particular, we evaluated the accuracy of the identified tibial mechanical axis and the repeatability of the obtained results. Tests performed by four surgeons on cadaveric knees showed that the variability in identifying the ankle center using two out of the three methods presented introduced an inaccuracy in the mechanical axis identification of around 1 degrees. This makes their use suitable for computer-assisted systems.
Principles of survey research (2002)

In this article, we discuss how to construct a questionnaire. We point out the need to use any previous research results to reduce the overheads of survey construction. We identify a number of issues to consider when selecting questions, constructing questions, deciding on the type of question and finalizing the format of the questionnaire.
Concentration Effects of Platelets, Fibrinogen and Thrombin on Platelet Aggregation and Fibrin Clotting (1974)

The effects of varying concentrations of platelets, fibrinogen and thrombin on platelet aggregation and on fibrin clotting were investigated. The results indicated that a threshold thrombin to platelet concentration ratio may be required to cause platelet activation. Above the threshold ratio, platelets exhibited properties which enhanced thrombin action in causing aggregation and fibrin clotting. At T/P ratios below the threshold level, the presence of platelets reduced thrombin activity, in other words, platelets exerted an antithrombin action. Fibrinogen at low concentrations (0.02-1.5 mg/ml) enhanced platelet aggregation induced by thrombin; whereas, at high concentrations of fibrinogen (2.0-4.0 mg/ml), aggregation was markedly inhibited. Continuous mixing of samples of paltelets and fibrinogen at physiological concentrations with thrombin at low concentrations (less than 2.0 U/ml) resulted in platelet aggregation. On the other hand, fibrin clots formed in samples without mixing or with high thrombin concentrations (greater than or equal to 5.0 U/ml). These results suggested that the quantitative relationships between platelets, fibrinogen and thrombin, and the presence or absence of cell contact may be important factors in determining the overall hemostasis.
Abstract 2690: Massively parallel multiplexed methods to screen hundreds of barcoded cancer cell line models with small molecules or genetic perturbations using next-generation sequencing (2019)

Abstract Phenotypic screening is a valuable tool to identify compounds to treat cancer, but is limited as it is time and resource intensive to screen hundreds of cancer cell lines. In order to increase the throughput of phenotypic screening, we set out to expand and further develop the PRISM method (Profiling Relative Inhibition Simultaneously in Mixtures) [Yu et al., 2016]. PRISM is a method to barcode cell lines with a unique 24 nucleotide barcode and mix them together to screen simultaneously in a pool, decreasing the time and cost of screening. The previously described PRISM method was limited in that it used only 100 adherent cell lines of one cancer model context, it required the use of a highly specialized Luminex bead-based detection system, and it was only applicable to small molecule screening. Here we report on the expansion of our barcoded cell line collection to 800 cancer cell lines of over 45 lineages, an improved method called PRISMseq using next-generation sequencing, and a novel method to perform genetic perturbations in 500 cancer cell lines simultaneously called PRISPR (PRISM/CRISPR). PRISMseq allows for assaying compound cell line sensitivity profiles in a large pool of hundreds of cell lines and detecting the DNA barcodes using next-generation sequencing (NGS). We recapitulate the known biology for established oncology drugs like the BRAF, EGFR, BCR-ABL and MDM2 inhibitor classes using this method with our cell line panel. We also further extended this method to be applicable to genetic perturbation using CRISPR/Cas9 knockout of individual genes concurrently in hundreds of cancer cell lines. We are able to recover expected biomarkers or genetic dependencies for our CRISPR/Cas9 validation reagents. This expanded PRISM profiling approach increases statistical power due to the addition of cancer contexts in our cell line collection, and improves versatility by enabling the screening of both small molecules and genetic perturbations. We believe that this method has overcome the limitations of the original PRISM method. It has also overcome the limitations of phenotypic screening, as the resources required to screen hundreds of cell lines has been decreased by orders of magnitude. Citation Format: Samantha Bender, Cong Zhu, Li Wang, Michael Rothberg, Joshua Dempster, Brenton Paolella, Mustafa Kocak, Massami Laird, Jordan Rossen, Karolina Stumbraite, Jordan Bryan, Vickie Wang, John Doench, Francisca Vazquez, Aviad Tsherniak, Todd Golub, Jennifer Roth. Massively parallel multiplexed methods to screen hundreds of barcoded cancer cell line models with small molecules or genetic perturbations using next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2690.