gebhart/patrepeval huggingface dataset:
P257 Real world experience of the new ACR-EULAR classification criteria for IgG4-related disease (2021)

<h3>Introduction</h3> IgG4-related hepatopancreatobiliary disease (IgG4-HPB) is part of a complex fibro-inflammatory systemic condition. It is critical to distinguish IgG4-HPB from malignant and inflammatory disease mimics to guide long-term management. The 2019 ACR/EULAR Classification Criteria for IgG4-related disease (IgG4-RD) were developed and validated in a large international cohort and reported to have excellent diagnostic specificity.<sup>1</sup> We sought to evaluate this in real-world clinical practice through our supra-regional Oxford-London IgG4-RD multi-disciplinary meeting (MDM). <h3>Methods</h3> We prospectively collected data on 153 patients referred to our IgG4-RD MDM over 4-years with suspected IgG4-RD (Clin Med, Jan 2020 <i>in press</i>). Each was classified as definite, possible or not IgG4-RD based on existing diagnostic criteria (HISORt, CDC, Boston Histopathology) and speciality experience. We retrospectively applied the ACR-EULAR classification criteria to this cohort to assess concordance with MDM outcomes. <h3>Results</h3> All cases considered not IgG4-RD in the MDM (n=52) similarly did not meet ACR/EULAR criteria. Of those considered definite IgG4-RD (n=63) in the MDM, only half (33;52%) met ACR/EULAR criteria. In those with definite HPB involvement (n=48) in the MDM, just over half (27;56%) met ACR-EULAR criteria. Most of the IgG4-HPB patients not meeting ACR/EULAR criteria scored insufficient diagnostic points (n=17) due to reliance on pancreatic imaging characteristics; diffuse swelling and pseudocapsule, with no points awarded for cholangiopathy without pancreatic involvement, atrophy, or focal enlargement of the gland. Small and unrepresentative biopsies were an additional challenge. Specific exclusions were absence of glucocorticoid response in advanced (fibrotic) cholangiopathy, and Crohn’s disease or ulcerative colitis in isolated HPB involvement. <h3>Conclusions</h3> The ACR-EULAR classification demonstrated excellent specificity (100%) and will be an invaluable tool for clinical trials. Disparity between diagnosis according to our IgG4-RD MDM and the ACR/EULAR criteria are explained by specific pancreatic imaging characteristics, absence of cholangiopathy/hepatopathy as a unique entity, and the necessity for steroid responsiveness even if presenting with advanced cholangiopathy. <h3>Reference</h3> Wallace ZS, Naden RP, Chari S, <i>et al</i>. The 2019 American College of Rheumatology/European League against Rheumatism classification criteria for IgG4-related disease. <i>Ann Rheum Dis</i> 2020;<b>79</b>:77–87. doi:10.1136/annrheumdis-2019-216561
Stabilized nanosystem of nanocarriers with an immobilized biological factor for anti-tumor therapy (2017)

The inadequate efficiency of existing therapeutic anti-cancer regiments and the increase in the multidrug resistance of cancer cells underscore the need to investigate novel anticancer strategies. The induction of apoptosis in tumors by cytotoxic agents produced by pathogenic microorganisms is an example of such an approach. Nevertheless, even the most effective drug should be delivered directly to targeted sites to reduce any negative impact on other cells. Accordingly, the stabilized nanosystem (SNS) for active agent delivery to cancer cells was designed for further application in local anti-tumor therapy. A product of genetically modified Escherichia coli, listeriolysin O (LLO), was immobilized within the polyelectrolyte membrane (poly(ethylenimine)|hyaluronic acid) shells of 'LLO nanocarriers' coupled with the stabilizing element of natural origin.
Recruitment and Activation of PTP1C in Negative Regulation of Antigen Receptor Signaling by FcγRIIB1 (1995)

Coligation of the Fc receptor on B cells, Fc gamma RIIB1, with the B cell antigen receptor (BCR) leads to abortive BCR signaling. Here it was shown that the Fc gamma RIIB1 recruits the phosphotyrosine phosphatase PTP1C after BCR coligation. This association is mediated by the binding of a 13-amino acid tyrosine-phosphorylated sequence to the carboxyl-terminal Src homology 2 domain of PTP1C and activates PTP1C. Inhibitory signaling and PTP1C recruitment are dependent on the presence of the tyrosine within the 13-amino acid sequence. Inhibitory signaling mediated by Fc gamma RIIB1 is deficient in motheaten mice which do not express functional PTP1C. Thus, PTP1C is an effector of BCR-Fc gamma RIIB1 negative signal cooperativity.
How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers? (1996)

We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise (CP) method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G(d,p) and D95++(d,p) basis sets at both the Hartree–Fock and second-order Mo/ller–Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the (more traditional) single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative (before vibrational corrections) and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone.
An Electronic Assistant for Scientific Investigation Working Prototype (1991)

Although many automated tools support the productivity of professionals (engineers, managers, architects, secretaries, etc.), none specifically address the needs of the scientific researcher. The scientist's needs are complex and the primary activities are cognitive rather than physical. The individual scientist collects and manipulates large data sets, integrates, synthesizes, generates, and records information. The means to access and manipulate information are a critical determinant of the performance of the system as a whole. One hindrance in this process is the scientist's computer environment, which has changed little in the last two decades. Extensive time and effort is demanded from the scientist to learn to use the computer system. A common paradigm that meets the critical requirement of facilitating information access and retrieval by the chemist is demonstrated. This paradigm was embodied in EASI, a working prototype that increased the productivity of the individual scientific researcher.
Imaging blood's velocity using synthetic aperture ultrasound (2012)

The blood velocity vector can be estimated using synthetic aperture techniques in medical ultrasound by using short emission sequences. The whole image region is insonified and the flow can be tracked in all directions continuously. This is a major advantage compared to commercial systems, since the separation between blood and tissue is greatly eased by this, and the estimates can be averaged over long time than in traditional systems. Vector velocity imaging can, thus, be made and attain an order of magnitude higher precision than in current commercial systems and at higher frame rates. It is also possible to visualize very slow moving flow. The paper will present methods for making such imaging.
Achieving uniform performance and maximizing throughput in the presence of heterogeneity (2011)

Continued scaling of process technologies is critical to sustaining improvements in processor frequencies and performance. However, shrinking process technologies exacerbates process variations - the deviation of process parameters from their target specifications. In the context of multi-core CMPs, which are implemented to feature homogeneous cores, within-die process variations result in substantially different core frequencies. Exposing such process-variation induced heterogeneity interferes with the norm of marketing chips at a single frequency. Further, application performance is undesirably dictated by the frequency of the core it is running on. To work around these challenges, a single uniform frequency, dictated by the slowest core, is currently chosen as the chip frequency sacrificing the increased performance capabilities of cores that could operate at higher frequencies. In this paper, we propose choosing the mean frequency across all cores, in lieu of the minimum frequency, as the single-frequency to use as the chip sales frequency. We examine several scheduling algorithms implemented below the O/S in hardware/firmware that guarantee minimum application performance near that of the average frequency, by masking process-variation induced heterogeneity from the end-user. We show that our Throughput-Driven Fairness (TDF) scheduling policy improves throughput by an average of 12% compared to a naive fairness scheme (round-robin) for frequency-sensitive applications. At the same time, TDF allows 98% of chips to maintain minimum performance at or above 90% of that expected at the mean frequency, providing a single uniform performance level to present for the chip.
Automation philosophy of a hybrid plant (2002)

A 4 layered philosophy compatible with industry standards such as ISA-S88.01, IEC1131 and ISO9001-3 has been applied throughout in automating an AECI Bioproducts Lysine plant with batch, semi-continuous and continuous sections. This paper outlines pertinent aspects of the process of creating robust, maintainable automation software.
Catheter-directed thrombolysis versus percutaneous mechanical thrombectomy in the management of acute limb ischemia: a single center review (2018)

PMT is associated with higher technical success and significantly shorter length of stay compared to CDT; however, clinical success is similar across both treatment entities. The safety profile is comparable.
A next-generation Internet federation object model for the HLA (2003)

This paper reports on development of a Web-based capability for distributed simulation in large-scale virtual environments that has been developed collaboratively by the Naval Postgraduate School and George Mason University. The work brings together several Years of effort in DIS-Java-VRML and the Virtual Reality Transfer Protocol on the part of NPS with a similar period of effort by GMU in selectively reliable multicast for distributed virtual simulation combined with Java-based middleware for use with the DoD High Level Architecture (HLA) for modeling and simulation. We describe the capability we have created for simulations of military and other highly interactive, physics-based models to operate in three-dimensional visualization over advanced Internet facilities. The major components of our system are described in detail, with the intent of creating interest in their use by the academic community.
Multidirectional tumor-suppressive activity of AIMP2/p38 and the enhanced susceptibility of AIMP2 heterozygous mice to carcinogenesis (2009)

Aminoacyl-transfer ribonucleic acid (tRNA) synthetases-interacting multifunctional protein (AIMP) 2 is a factor associated with the macromolecular protein synthesis machinery consisting of nine different aminoacyl-tRNA synthetases and three non-enzymatic factors. However, it was shown to work as a multifaceted regulator through the versatile interactions with diverse signal mediators. For instance, it can mediate pro-apoptotic response to DNA damage and tumor necrosis factor-alpha (TNF-alpha) stimulus and growth-arresting signal by transforming growth factor (TGF)-beta. Considering that these pathways are critically implicated in the control of tumorigenesis, AIMP2 is expected to work as a potent tumor suppressor with broad coverage against different cancer types. Here we investigated whether AIMP2 would give gene dosage effect on its pro-apoptotic and anti-proliferative activities using the wild-type, hetero- and homozygous AIMP2 cells and whether AIMP2 would be critical in preventing tumorigenesis using different in vivo tumor models. Both the apoptotic responses to DNA damage and TNF-alpha and sensitivity to growth arresting TGF-beta signal were reduced in AIMP2 hetero- and homozygous cells compared with the wild-type cells in dose-dependent manner. In all the in vivo carcinogenesis experiments, reduction of AIMP2 level in heterozygous AIMP2 mice provided higher susceptibility to tumor formation. Thus, this work proves the functional significance of AIMP2 in determination of cell proliferation and death, and as a haploinsufficient tumor suppressor.
Collision avoidance using artificial retina sensor in ALV (2002)

The artificial retina sensor (ARS) which was developed at Osaka University in Japan, is applied to PRV II (POSTECH Road Vehicle II) for real time collision avoidance in high speed navigation. ARS consists of a linear CCD sensor and a dove prism rotating in front of the camera lens. Since ARS provides polar domain images directly from the scene, size and projection invariance in a polar coordinate system can be utilized directly. Thus one only has to apply an edge detection and a template matching method to the horizontal direction. Then optical-flow of moving objects is estimated to obtain 3D distance and time-to-impact informations from obstacles. To verify the validity of the the authors' proposed technique, real images are taken using an ARS mounted on PRV II and analyzed.
Rates of various reactions catalyzed by ATP synthase as related to the mechanism of ATP synthesis. (1991)

The forward and reverse rates of the overall reaction catalyzed by the ATP synthase in intact rat heart mitochondria, as measured with 32P, were compared with the rates of two partial steps, as measured with 18O. Such rates have been measured previously, but their relationship to one another has not been determined, nor have the partial reactions been measured in intact mitochondria. The partial steps measured were the rate of medium Pi formation from bound ATP (in state 4 this also equals the rate of medium Pi into bound ATP) and the rate of formation of bound ATP from bound Pi within the catalytic site. The rates of both partial reactions can be measured by 31P NMR analysis of the 18O distribution in Pi and ATP released from the enzyme during incubation of intact mitochondria with highly labeled [18O]Pi. Data were obtained in state 3 and 4 conditions with variation in substrate concentrations, temperature, and mitochondrial membrane electrical potential gradient (delta psi m). Although neither binding nor release of ATP is necessary for phosphate/H2O exchange, in state 4 the rate of incorporation of at least one water oxygen atom into phosphate is approximately twice the rate of the overall reaction rate under a variety of conditions. This can be explained if the release of Pi or ATP at one catalytic site does not occur, unless ATP or Pi is bound at another catalytic site. Such coupling provides strong support for the previously proposed alternating site mechanism. In state 3 slow reversal of ATP synthesis occurs within the mitochondrial matrix and can be detected as incorporation of water oxygen atoms into medium Pi even though medium [32P]ATP does not give rise to 32Pi in state 3. These data can be explained by lack of translocation of ATP from the medium to the mitochondrial matrix. The rate of bound ATP formation from bound Pi at catalytic sites was over twice the rate of the overall reaction in both states 4 and 3. The rate of reaction at the catalytic site is considerably less sensitive to the decrease in membrane potential and the concentration of medium ADP than is the rate of medium ATP formation. This supports the view that the active catalytic site is occluded and proceeds at a rapid rate which is relatively independent of delta psi m and of media substrates.
[Validation of Oscillomat, a device for self-measurement of blood pressure. Comparison with mercury sphygmomanometers]. (1991)

Self-measurement of arterial blood pressure (BP) is a valuable aid in the follow-up of hypertensive patients. Unfortunately, the devices utilized are not subject to certification and therefore must be validated. In this study, the accuracy and precision of BP measurement with the Oscillomat device were measured and simultaneously compared with those of a standard mercury sphygomomanometer in 60 subjects and with a random zero mercury sphygmomanometer in 44 subjects. The Oscillomat device correctly explored systolic and diastolic BP within a 55 to 210 mmHg range. Compared with the auscultatory method, it tended to underestimate systolic BP values by + 3 to -15 mmHg and diastolic B.P. values by + 1 to -15 mmHg.
Subpicosecond GaAs Wafer Probe System (1993)

We report a subpicosecond GaAs wafer probe system which incorporates a mechanical flexure and a micromachined GaAs IC for time domain on-wafer measurements. The micromachined GaAs IC incorporates a novel high speed pulse sharpener and a two diode sampling bridge with a micromachined GaAs tip.
Twenty-five years of bis-pentafluorophenyl borane: a versatile reagent for catalyst and materials synthesis (2019)

In 1995, the synthesis, properties and remarkable hydroboration activity of bis-pentafluorophenyl borane was first reported. Its reactivity stems from the ready accessibility of the monomeric borane and its high Lewis acidity. In the intervening twenty five years, this reagent has been widely exploited as a means of incorporating Lewis acidic -B(C6F5)2 groups into complex structures for a range of applications. In this "25th Anniversary" Feature article, we highlight the synthetic methods to the borane, its fundamental properties and chemistry as well as the diverse array of uses of this borane. These include self-activating olefin polymerization catalysts, frustrated Lewis pair generation, small molecule activation, bond cleavage reactions, Lewis acid catalysis and modification of organic materials.
MRI-US fusion targeted biopsy results in men with a history of prior cancer. (2016)

88 Background: Appropriate risk stratification of men on active surveillance for prostate cancer is essential to identify men in whom it is safe to take this deferred treatment approach. This study evaluates upstaging rates using MRI-US fusion targeted biopsy in men who have had a prior positive standard 12-core biopsy. Methods: Between 12/2012 and 06/2015, 374 men with an indication for prostate biopsy underwent pre-biopsy mpMRI followed by 12-core standard trans-rectal mapping biopsy (Mbx) and MRI-Ultrasound fusion targeted biopsy (Tbx) of lesions identified on mpMRI. The combination of Mbx and Tbx, when both occurred, constitutes a fusion biopsy (Fbx). Men who underwent both Mbx with or without Tbx using the Artemis/Pro-Fuse system with a previous non-MRI-guided biopsy and a diagnosis of prior Gleason 6 prostate cancer were included. Patients without a lesion on MRI underwent Mbx only. Maximum Gleason scores (GS) were assigned on a per patient basis with Mbx GS available for all patients in the cohort and Tbx GS available only for patients with a lesion visible on MP-MRI. Clinically significant (CS) cancer was defined as GS ≥ 3+4. GS per patient was compared by chi-square and McNemar’s test. Results: 118 patients met inclusion criteria (Mean PSA = 6.9, Mean age = 62.5). 40 patients (34%) were upstaged by Fbx to Gleason ≥ 7. Of those upstaged, 17 men (14%) would have been missed by Mbx alone, in comparison to 7 (6%) that were missed by Tbx alone. Total number of prior biopsies (p = 0.28) and number of years on Active Surveillance (p = 0.22) were not related to upgrade on Fbx. Older men (65.3 vs. 60.9, p = 0.033) and those with higher PSA (8.7 vs 5.8, p = 0.002) were more likely to be upgraded on Fbx. Tbx was more likely to identify CS cancer than Mbx (85% vs 56%; p &lt; 0.012). Conclusions: MP-MRI Fusion biopsy more accurately stratifies men with a previous prostate biopsy than those receiving a template mapping 12-core biopsy alone. Tbx should be strongly considered before enrolling a patient in active surveillance since up 14% of clinically significant cancer would have been missed with a 12-core biopsy alone. [Table: see text]
How Will Copper Contamination Constrain Future Global Steel Recycling? (2017)

Copper in steel causes metallurgical problems, but is pervasive in end-of-life scrap and cannot currently be removed commercially once in the melt. Contamination can be managed to an extent by globally trading scrap for use in tolerant applications and dilution with primary iron sources. However, the viability of long-term strategies can only be evaluated with a complete characterization of copper in the global steel system and this is presented in this paper. The copper concentration of flows along the 2008 steel supply chain is estimated from a survey of literature data and compared with estimates of the maximum concentration that can be tolerated in steel products. Estimates of final steel demand and scrap supply by sector are taken from a global stock-saturation model to determine when the amount of copper in the steel cycle will exceed that which can be tolerated. Best estimates show that quantities of copper arising from conventional scrap preparation can be managed in the global steel system until 2050 assuming perfectly coordinated trade and extensive dilution, but this strategy will become increasingly impractical. Technical and policy interventions along the supply chain are presented to close product loops before this global constraint.
Adoptive Cell Transfer and Vaccines in Melanoma: The Horizon Comes Into View (2022)

Over the past four decades, cancer immunotherapy for melanoma has evolved from single-agent, type-I cytokine therapy to combination immune checkpoint inhibition. Along the way, breakthroughs in the fields of cell therapy and cancer vaccination have been made as well. The early data from adoptive cell therapy, involving the delivery of tumor infiltrating lymphocytes harvested from resected tumors, was generated at the National Cancer Institute. Subsequently, a limited number of centers across the globe have developed programs to deliver these therapies. Recently, more widespread availability of this therapy has been made possible by centralizing the growth and expansion of tumor infiltrating lymphocyte products, then distributing the products for delivery of therapy at numerous academic medical centers. Work is ongoing to optimize these treatments with additional cell types and/or modified cell products, and to determine the best ways of combining these treatments with immune checkpoint inhibition. Similarly, tumor vaccination strategies are undergoing dramatic changes, transitioning the field from peptide-based vaccines to next-generation sequencing and T-cell receptor sequencing. These changes help improve the selection of targeted antigens by finding more immunogenic options, and they help with the development of lipid nanoparticles and mRNA delivery. In short, evolution of the approaches that are revolutionizing infectious disease vaccination has been ongoing, and there are promising preliminary data in patients with melanoma.
OCT utilization: Summary statistics from the LightLab clinical initiative (2022)

After completion of the standardized OCT-guided workflow, there was greater uptake of OCT imaging, incorporation in more complex procedures, procedural efficiency, and image quality.