gebhart/patrepeval huggingface dataset:
Data from Antitumor Efficacy of the Novel KIT Inhibitor IDRX-42 (Formerly M4205) in Patient- and Cell Line–Derived Xenograft Models of Gastrointestinal Stromal Tumor (GIST) (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;The majority of gastrointestinal stromal tumors (GIST) are driven by constitutively activated KIT/PDGFRA kinases and are susceptible to treatment with tyrosine kinase inhibitors. During treatment, most of these tumors will develop secondary mutations in &lt;i&gt;KIT&lt;/i&gt; or &lt;i&gt;PDGFRA&lt;/i&gt; inducing drug resistance, so there is an unmet need for novel therapies. We tested the efficacy of IDRX-42, a novel selective KIT inhibitor with high activity toward the most relevant &lt;i&gt;KIT&lt;/i&gt; mutations, in 4 GIST xenograft models.&lt;/p&gt;Experimental Design:&lt;p&gt;NMRI &lt;i&gt;nu/nu&lt;/i&gt; mice were transplanted with patient-derived GIST xenograft models UZLX-GIST9 (&lt;i&gt;KIT&lt;/i&gt;:p.P577del;W557LfsX5;D820G), UZLX-GIST2B (&lt;i&gt;KIT&lt;/i&gt;:p.A502_Y503dup), UZLX-GIST25 (&lt;i&gt;KIT&lt;/i&gt;:p.K642E), and the cell line–derived model GIST882 (&lt;i&gt;KIT&lt;/i&gt;:p.K642E). Mice were treated daily with vehicle (control), imatinib (100 mg/kg), sunitinib (20 mg/kg), avapritinib (5 mg/kg), or IDRX-42 (10 mg/kg, 25 mg/kg). Efficacy was assessed by tumor volume evolution, histopathology, grading of histologic response, and IHC. The Kruskal–Wallis and Wilcoxon matched-pairs tests were used for statistical analysis, with &lt;i&gt;P&lt;/i&gt; &lt; 0.05 considered as significant.&lt;/p&gt;Results:&lt;p&gt;IDRX-42 (25 mg/kg) caused tumor volume shrinkage in UZLX-GIST25, GIST882, and UZLX-GIST2B, with a relative decrease to 45.6%, 57.3%, and 35.1% on the last day as compared with baseline, and tumor growth delay (160.9%) compared with control in UZLX-GIST9. Compared with controls, IDRX-42 (25 mg/kg) induced a significant decrease in mitosis. In UZLX-GIST25 and GIST882 grade 2–4 histologic response with myxoid degeneration was observed in all IDRX-42 (25 mg/kg)-treated tumors.&lt;/p&gt;Conclusions:&lt;p&gt;IDRX-42 showed significant antitumor activity in patient- and cell line–derived GIST xenograft models. The novel kinase inhibitor induced volumetric responses, decreased mitotic activity, and had antiproliferative effects. In models with &lt;i&gt;KIT&lt;/i&gt; exon 13 mutation IDRX-42 induced characteristic myxoid degeneration.&lt;/p&gt;&lt;/div&gt;
Mechanical properties of CrN-based superlattices: Impact of magnetism (2021)

Superlattices represent an important design concept for materials with exceptional properties. In this work, we report on the influence of different interface orientations and magnetic configurations of CrN in B1 CrN/(TiN,AlN) superlattices on their mechanical and the structural properties studied with the help of density functional theory. The oscillations of interplanar spacings, formerly linked to the cleavage strength in similar material systems, were found to be in no correlation with the magnetic moments of individual CrN planes. An explicit consideration of the interfaces is important for an accurate estimation of elastic constants. In this context, the continuum mechanics-based Grimsditsch and Nizzoli method ignoring interface properties yields even qualitatively wrong results. Similarly, our calculations show that the ferromagnetic state of CrN as an approximation of (computationally much more demanding) paramagnetic magnetic state does not provide correct predictions of the material behaviour. In other words, explicit treatment of the magnetic moments as well as the interfaces is necessary for qualitatively correct modelling of CrN-based superlattices. Finally, the theoretically predicted elastic constants and fracture toughness values were corroborated by CrN/TiN micro-cantilever experiments.
Stereocontrolled synthesis of deuterated phenylalanine derivatives through manipulation of an N-phthaloyl protecting group for the recall of stereochemistry. Application in the study of phenylalanine ammonia lyase (2001)

The enantiomers of [2-2 H 1 ]phenylalanine and all four stereoisomers of [2,3-2 H 2 ]phenylalanine have been prepared from (S)-phenylalanine through the introduction of a chiral centre onto an Nphthaloyl protecting group for the recall of stereochemistry. Studies of the interaction of these labelled phenylalanines with (S)-phenylalanine ammonia lyase show that both the C-2 and C-3 hydrogens of the product trans-cinnamate undergo exchange with solvent in the presence of the enzyme. The mechanistic implications of this observation are discussed.
Multiple Reaction Monitoring Mass Spectrometry for the Discovery and Quantification of O-GlcNAc-Modified Proteins (2013)

O-linked N-acetylglucosamine (O-GlcNAc) is a post-translational modification regulating proteins involved in a variety of cellular processes and diseases. Unfortunately, O-GlcNAc remains challenging to detect and quantify by shotgun mass spectrometry (MS) where it is time-consuming and tedious. Here, we investigate the potential of Multiple Reaction Monitoring Mass Spectrometry (MRM-MS), a targeted MS method, to detect and quantify native O-GlcNAc modified peptides without extensive labeling and enrichment. We report the ability of MRM-MS to detect a standard O-GlcNAcylated peptide and show that the method is robust to quantify the amount of O-GlcNAcylated peptide with a method detection limit of 3 fmol. In addition, when diluted by 100-fold in a trypsin-digested whole cell lysate, the O-GlcNAcylated peptide remains detectable. Next, we apply this strategy to study glycogen synthase kinase-3 beta (GSK-3β), a kinase able to compete with O-GlcNAc transferase and modify identical site on proteins. We demonstrate that GSK-3β is itself modified by O-GlcNAc in human embryonic stem cells (hESC). Indeed, by only using gel electrophoresis to grossly enrich GSK-3β from whole cell lysate, we discover by MRM-MS a novel O-GlcNAcylated GSK-3β peptide, bearing 3 potential O-GlcNAcylation sites. We confirm our finding by quantifying the increase of O-GlcNAcylation, following hESC treatment with an O-GlcNAc hydrolase inhibitor. This novel O-GlcNAcylation could potentially be involved in an autoinhibition mechanism. To the best of our knowledge, this is the first report utilizing MRM-MS to detect native O-GlcNAc modified peptides. This could potentially facilitate rapid discovery and quantification of new O-GlcNAcylated peptides/proteins.
Geometrical principles in the construction of molecular structures of heterometallic alkoxide complexes (2002)

We obtained two dinuclear Nickel(II) complexes having different N3 ligand binding type; [Ni2 (L-Et)(N3)(H2O)](NO3) .2H2O (1) (where: HL-Et=N,N,N'N'tetrakis [(1-ethyl-2benzimidazolyl)methyl]-2-hydroxy-1,3-diaminopropane) and [Ni2 (L-Et)(N3)(H2O) ](NO3) .2C2H5OH (2), respectively. Complex 1 is synthesized from HL-Et, Ni(NO3).6H2O, NaOH and NaN3 in MeOH , indicating week antiferromagnetic interaction. 2 is synthesized from the quite same reagent as 1 with equivalent amount but in different solvent ; EtOH, indicating strong antiferromagnetic interaction. We undertook the X-ray structural analyses of 1 and 2 to elucidate the crystal structures causing the different magnetic susceptibility. Crystal Data: C43H59O12N15Ni2, (1), F.W. = 1095.4, monoclinic, P21/c, a = 13.751(1)4 , b = 24.356(1), c = 17.006(1), = 100.19(1) , V = 5606(1) 3 Z = 4, Dc = 1.298 g cm -3 , (MoK) = 7.39cm -1 -, F(000) = 2296, R (Rw)= 0.089(0.119). C47H65O11N15Ni2, (2) F.W. = 1133.5, triclinic, P-1, a = 17.112(1). , b =17.222(1), c =10.296(1) , = 102.957(2), =103.413(2), = 64.233(1) , V = 2632(1) 3 , Z = 2, Dc = 1.430 g cm -3 , (MoK ) = 7.88 cm -1 , F(000) = 1192, R (Rw) = 0.072(0.060). It is observed that 1 has the conformation with N3 ligand being monodentated to one Ni atom, on the other hand, 2 has the conformation with N3 ligand being end-to-end bridging to two Ni atoms.
High pressure/high temperature thermogravimetric apparatus. Final report (1999)

The purpose of this instrumentation grant was to acquire a state-of-the-art, high pressure, high temperature thermogravimetric apparatus (HP/HT TGA) system for the study of the interactions between gases and carbonaceous solids for the purpose of solving problems related to coal utilization and applications of carbon materials. The instrument that we identified for this purpose was manufactured by DMT (Deutsche Montan Technologies)--Institute of Cokemaking and Coal Chemistry of Essen, Germany. Particular features of note include: Two reactors: a standard TGA reactor, capable of 1100 C at 100 bar; and a high temperature (HT) reactor, capable of operation at 1600 C and 100 bar; A steam generator capable of generating steam to 100 bar; Flow controllers and gas mixing system for up to three reaction gases, plus a separate circuit for steam, and another for purge gas; and An automated software system for data acquisition and control. The HP/TP DMT-TGA apparatus was purchased in 1996 and installed and commissioned during the summer of 1996. The apparatus was located in Room 128 of the Prince Engineering Building at Brown University. A hydrogen alarm and vent system were added for safety considerations. The system has been interfaced to an Ametek quadruple mass spectrometer (MA 100), pumped by a Varian V250 turbomolecular pump, as provided for in the original proposed. With this capability, a number of gas phase species of interest can be monitored in a near-simultaneous fashion. The MS can be used in a few different modes. During high pressure, steady-state gasification experiments, it is used to sample, measure, and monitor the reactant/product gases. It can also be used to monitor gas phase species during nonisothermal temperature programmed reaction (TPR) or temperature programmed desorption (TPD) experiments.
Intraperitoneally Delivered Umbilical Cord Lining Mesenchymal Stromal Cells Improve Survival and Kidney Function in Murine Lupus via Myeloid Pathway Targeting (2022)

To determine the therapeutic efficacy of human umbilical cord lining mesenchymal stromal cells (CL-MSCs) (US Patent number 9,737,568) in lupus-prone MRL/lpr (Fas<sup>lpr</sup>) mice and elucidate its working mechanisms. A total of 4 doses of (20-25) × 10<sup>6</sup> cells/kg of CL-MSCs was given to 16-week-old female Fas<sup>lpr</sup> mice by intraperitoneal injection. Three subsequent doses were given on 17 weeks, 18 weeks, and 22 weeks, respectively. Six-week-old Fas<sup>lpr</sup> mice were used as disease pre-onset controls. Mice were monitored for 10 weeks. Mouse kidney function was evaluated by examining complement component 3 (C3) deposition, urinary albumin-to-creatinine ratio (ACR), and lupus nephritis (LN) activity and chronicity. Working mechanisms were elucidated by flow cytometry, Luminex/ELISA (detection of anti-dsDNA and isotype antibodies), and RNA sequencing. CL-MSCs improved mice survival and kidney function by reducing LN activity and chronicity and lymphocyte infiltration over 10 weeks. CL-MSCs also reduced urinary ACR, renal complement C3 deposition, anti-dsDNA, and isotype antibodies that include IgA, IgG1, IgG2a, IgG2b, and IgM. Immune and cytokine profiling demonstrated that CL-MSCs dampened inflammation by suppressing splenic neutrophils and monocytes/macrophages, reducing plasma IL-6, IL-12, and CXCL1 and stabilizing plasma interferon-γ and TNF-α. RNA sequencing further showed that CL-MSCs mediated immunomodulation via concerted action of pro-proinflammatory cytokine-induced chemokines and production of nitric oxide in macrophages. CL-MSCs may provide a novel myeloid (neutrophils and monocytes/macrophages)-targeting therapy for SLE.
Test data for the calculation of powder paterns for intermetallic phases (1996)

The antihypertensive response with estradiol was the same as with captopril in the premenopausal patient with systemic hypertension.
Signal-to-noise-ratio loss in hearing-impairment and feature enhancement. (2009)

The primary purpose of this study is to investigate detailed consequences of hearing loss and to scrutinize if individual hearing impaired (HI) listeners exhibit individual patterns in their consonant confusion scores. 16 English nonsense CV syllables, by 18 various talkers in five speech-weighted noise (−12, −6, 0, +6, and +12-dB signal-to-noise-ratios) and quiet conditions, were randomly presented to 11 HI subjects (18 HI ears) having sensorineural hearing losses at two different amplified levels: with and without NAL-R (similar to fitting hearing aids). The HI ears have sensorineural hearing loss with flat (mild-to-moderate-to-severe), ski-slop at low- and/or high-frequency regions, and cookie-bite configurations. To characterize the consonant loss, the performance of each HI ear was compared to average normal-hearing listeners in masking noise. Preliminary analysis shows that each HI ear has an individual profile, which is a characteristic of the impaired ear. Once the noise-sensitive consonants are identified, the aim is to use signal processing techniques to selectively enhance features to make them audible in noise. [Work supported by the NIH Grant RDC009277A.]
Lack of evidence for a superantigen in lymphocytes from HIV-discordant monozygotic twins (1994)

Our results suggest that PBMC from the two HIV-infected twins do not express a functionally detectable SAg.
Doing Inclusive Design (2020)

How can user interface and user experience (UI/UX) professionals assess whether their software supports diverse users? And if they find problems, how can they fix them? We begin this keynote address with a summary of GenderMag, a systematic inspection method for finding and fixing "gender inclusivity bugs---biases against different genders in software interfaces and workflows. We then show what UI/UX professionals are doing with it in the real world, from their bias finds & fixes to their practices & pitfalls in using it. Finally, we present InclusiveMag, a meta-method that can be used by HCI researchers to generate systematic inclusiveness methods for other dimensions of diversity.
Characterization of an underwater metamaterial made of aluminum honeycomb panels at low frequencies (2021)

This paper presents a method to characterize the effective properties of inertial acoustic metamaterial unit cells for underwater operation. The method is manifested by a fast and reliable parameter retrieval procedure utilizing both numerical simulations and measurements. The effectiveness of the method was proved to be self-consistent by a metamaterial unit cell composed of aluminum honeycomb panels with soft rubber spacers. Simulated results agree well with the measured responses of this metamaterial in a water-filled resonator tube. A sub-unity density ratio and an anisotropic mass density are simultaneously achieved by the metamaterial unit cell, making it useful in implementations of transformation acoustics. The metamaterial, together with the approach for its characterization, are expected to be useful for underwater acoustic devices.
Magnetic Nanostructures Patterned by Focused Ion Beam in an ultrathin Pt/Co/Pt film (2002)

The magnetic properties of Co/Pt films can be modified and even controlled by ion beam irradiation. For example, the coercivity and magnetic anisotropy of a 1.4nm thick Co layer are reduced with increasing the Ga+ ion dose. Images of the demagnetized states and remanent hysteresis loops are obtained for arrays of dots or tracks patterned by the focused ion beam technique. 20 nm wide sharp non-magnetic irradiated lines separate the magnetic dots or the tracks, the size of the dots or the width of the tracks varying from 1.8 μm down to 70 nm. The efficiency of the dipolar interaction is studied, and the use of such dot arrays for magnetic or magneto-optical recorrding discussed.
ML-based estimation of the number of devices in industrial networks using unlicensed bands (2022)

Advanced automation is being adopted by manu-facturing facilities and wireless technologies are set to be a key component in driving the factories of the future. It is expected that private cellular networks and WLAN technologies would be deployed for smart factory operations. Since both wireless technologies can operate on the same channel in unlicensed bands, then efficient resource sharing becomes important. When multiple devices compete for the resource, the estimation of number of devices contending for the channel resource can help the design of an efficient resource sharing scheme. This paper aims to address the challenge of estimating the number of factory devices contending to transmit over the unlicensed channel. We adopt three machine learning (ML) techniques and develop a novel device number estimation system by collating and analysing the idle-time interval between transmission across the channel. By using NS-3 simulation, the performance of the proposed estimation approach is evaluated. The results presented reveal the significance of the chosen features and performance of each ML algorithm used.
PERFORMANCE EVALUATION AND CALIBRATION OF THE NEURO-PET SCANNER (1983)

Sank, V. J.; Brooks, R. A.; Friauf, W. S.; Leighton, S. B.; Cascio, H. E.; Chiro, G. Di Author Information
Direct ethanol injection for skull metastasis from hepatocellular carcinoma. The techniques and consequences of a therapeutic trial (1998)

The frequency of skull metastasis from hepatocellular carcinoma (HCC) is increasing together with the recent progress in the management of the primary lesion. Cases are often complicated with poor general conditions or metastasis to the other organs, and not readily indicated for surgery. A direct injection of ethanol to the lesion could be one of the therapeutic options to cope with this complicated situation. To evaluate the feasibility of this technique, we planned a therapeutic trial in a patient with HCC associated with lumbar and skull metastasis, the latter metastasis repeated twice during the past one year. A total of 10 ml of ethanol was injected into the skull metastasis percutaneously under ultrasound (US) guidance. US guidance was very useful in determining the sites of injections and the distribution of ethanol as well as monitoring the blood flow within the tumor vessels. The patient transiently complained of local pain at the injection sites, but there were no other adverse effects. Four days after the injection, the lesion was resected by surgery, which confirmed the pathologic diagnosis as well as the nearly-total necrosis of the tumor. This technique is simple, safe and repeatable with low cost. The technical details and the histologic effects are described.
B-49 | Mitral Annular Calcification: Prevalence, Characteristics, and Impact on Outcomes Following Transcatheter Aortic Valve Replacement – A Systematic Review and Meta-Analysis (2023)

There is a paucity of data on the prognostic impact of mitral annular calcification (MAC) in patients undergoing transcatheter aortic valve replacement (TAVR) with conflicting results being reported by the studies that are published We performed a meta-analysis to assess the short-term and long-term outcomes of MAC in post-TAVR patients. Of 25,407 studies identified after the initial database search, four observational studies comprising of 2,620 patients (2,030 patients in the non-severe MAC arm and 590 patients in the severe-MAC arm) were included in the final analysis Compared to patients with non-severe MAC, severe MAC group was associated with significantly higher incidences of overall bleeding (0.75 [0.57, 0.98], p=0.03, I2=0%) at 30-days. However, no significant difference was observed between the two groups for rest of the 30-day outcomes: all-cause mortality (0.79 [0.42, 1.48], p=0.46, I2=9%), myocardial infarction (1.62 [0.37, 7.04], p=0.52, I2=0%), cerebrovascular accident or stroke (1.22 [0.53, 2.83], p=0.64, I2=0%), acute kidney injury (1.48 [0.64, 3.42], p=0.35, I2=0%), and pacemaker implantation (0.70 [0.39, 1.25], p=0.23, I2=68%). Similarly, follow-up outcomes also showed no significant difference between the two groups: all-cause mortality (0.69 [0.46, 1.03], p=0.07, I2=44%), cardiovascular mortality (0.52 [0.24, 1.13], p=0.10, I2=70%) and stroke (0.83 [0.41, 1.69], p=0.61, I2=22%). The sensitivity analysis, however, demonstrated significant results for all-cause mortality (0.57 [0.39, 0.84], p=0.005, I2=7%) by removing the study by Okuno et al and cardiovascular mortality (0.41 [0.21, 0.82], p=0.01, I2=66%) by removing the study by HM Lak et al. Our meta-analysis corroborates the notion that isolated MAC is not an independent predictor of long-term mortality after TAVR and determines severe MAC to be a strong predictor of mortality at follow-up due to higher incidence of mitral valve dysfunction associated with it.
Observer Design for Downsized Gasoline Engine Control Using 1D Engine Simulation (2006)

This study presents the use of a 1D engine model for the control design of a twin-scroll turbocharged gasoline direct injection 2.0 l i4 engine with twin camphaser. This virtual engine is used for the development of the in-cylinder mass observer which is a crucial issue for the control of such an engine because of the large scavenging effects. After the model calibration process based on bench results, the virtual engine reproduces with accuracy the major behaviour such as valve overlap effects on cylinder filling and combustion which are an important feature for engine control with such advanced technology. Finally, thanks to the engine model contribution, the in-cylinder mass controller/observer design can be made easier and is validated off-line at a first stage. The goal of the paper is to demonstrate the relevancy of using 1D engine simulation as a support tool during all the steps of the engine control development process from design to real-time validation.
Supplementary Table 2 from Prospective Blinded Study of &lt;i&gt;BRAF&lt;/i&gt;&lt;sup&gt;V600E&lt;/sup&gt; Mutation Detection in Cell-Free DNA of Patients with Systemic Histiocytic Disorders (2023)

&lt;p&gt;Supplemental Table 2: Concordance of initial plasma cell-free DNA (cfDNA) assessment of BRAFV600E mutations with tissue biopsy BRAFV600E result.&lt;/p&gt;
Establishing Standards for Centers of Excellence for the Diagnosis and Treatment of Lymphatic Disease (2021)

<b><i>Background:</i></b> Lymphatic disease patients make up a significant proportion of the US and world populations. Due to inadequate medical school training and underestimation of the impact of lymphatic circulation, lymphatic disease patients often have difficulty finding competent diagnosis and care. <b><i>Methods and Results:</i></b> The Lymphatic Education & Research Network has initiated a Centers of Excellence program to designate institutions that provide services for lymphatic disease patients. Committees of experts drafted standards for five types of Centers of Excellence. <b><i>Conclusions:</i></b> The Centers of Excellence program is now launched, and the description of the formation process herein could provide other organizations guidance for similar ventures.