gebhart/patrepeval huggingface dataset:
A phase I study of IV aflibercept (Afl) in combination with R-CHOP in untreated patients (pts) with B-cell lymphoma. (2010)

8010 Background: In malignant lymphoma, angiogenesis has been associated with adverse outcome or more aggressive clinical behavior. This correlation has been established in groups of patients with a large heterogeneity regarding lymphoma subtypes and treatment regimens. Afl is an angiogenesis inhibitor that inactivates circulating VEGF. Methods: This phase I study was designed to evaluate the safety and preliminary anti- tumor activity of Afl when administered in combination with R-CHOP every 3 weeks (R-CHOP21), for 6-8 cycles in B-cell lymphoma. Biomarkers (endogenous VEGF, CD31, CD34, microvessel density, VEGF-R, endothelial progenitor cells) were also explored. Results: Between March 2008 and March 2009, 25 pts (M/F 15/10), median age 62 (range 37-78), were treated with Afl dose levels of 3 mg/kg (DL1, N=3) and 6 mg/kg (DL2, N=22) combined with R-CHOP21. Lymphoma histology types were: diffuse large B-cell (DLBCL) (N=15), follicular (N=8), mantle cell (N=1) and marginal zone (N=1). The Ann Arbor stage at diagnosis was I-II (7 pts) and III-IV (18 pts). Eighty percent of pts had elevated endogenous VEGF values at baseline (superior to 30 pg/mL).Main grade 3 or 4 study drug related AEs included hypertension (N=8), febrile neutropenia (N=4) and asthenia (N=4) and were present only at dose level 6 mg/kg. One dose limiting toxicity at DL2 was observed: grade 3 headache and arthralgia. No proteinuria and no other major cardiovascular events were reported.Main specific related AE was grade 1/2 reversible dysphonia (18 pts). Response rate at the end of the treatment based on IWC and PET criteria (Cheson. JCO. 2007.) was: 80% complete responses and 20% partial responses. PFS and biomarkers data will be provided. Conclusions: The selected dose of 6 mg/kg of Afl used in all on-going phase III trials in combination with R-CHOP21 is feasible and well tolerated in B-cell lymphoma. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration sanofi-aventis sanofi-aventis
Delamination Strengths of Different Types of REBCO-Coated Conductors and Method for Reducing Radial Thermal Stresses of Impregnated REBCO Pancake Coils (2015)

An impregnated pancake coil is composed of a REBa <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7-δ</sub> (REBCO)-coated conductor, a polyimide tape, and epoxy resin, so that a radial thermal stress is generated in the winding by their anisotropic thermal contraction when the coil is cooled from room temperature to 77 K or less. If this radial stress locally exceeds the delamination strength of the REBCO-coated conductor under transverse tensile stress, the coil will be degraded. Although it is important to determine the exact delamination strength of the REBCO-coated conductor to fabricate an impregnated coil that does not suffer from degradation, the delamination strengths reported until now have shown considerable variation due to the evaluation methods used. Therefore, we propose a new method for evaluating the delamination strength using small epoxy impregnated test coils, since the radial stress depends on the ratio of inner to outer diameters regardless of the coil size. The delamination strength can be obtained by investigating the ratios of inner to outer diameters that do not result in degradation. In this paper, the delamination strengths of three types of REBCO-coated conductors made with different manufacturing processes and having different configurations were evaluated. This method showed that a conductor laminated with copper plates had higher delamination strength than the other two kinds of conductors. In addition, impregnated single pancake coils whose inner diameter was 50 mm and whose outer diameter was 100 mm were fabricated using the three types of REBCO-coated conductors. Degradation was avoided in all coils by dividing the coils into a number of winding parts in the radial direction according to the delamination strength of the conductors.
Occurrence of a d-arabinose-containing complex-type free-N-glycan in the urine of cancer patients (2022)

Urinary free-glycans are promising markers of disease. In this study, we attempted to identify novel tumor markers by focusing on neutral free-glycans in urine. Free-glycans extracted from the urine of normal subjects and cancer patients with gastric, colorectal, pancreatic and bile duct were fluorescently labeled with 2-aminopyridine. Profiles of these neutral free-glycans constructed using multidimensional high performance liquid chromatography separation were compared between normal controls and cancer patients. The analysis identified one glycan in the urine of cancer patients with a unique structure, which included a pentose residue. To reveal the glycan structure, the linkage fashion, monosaccharide species and enantiomer of the pentose were analyzed by high performance liquid chromatography and mass spectrometry combined with several chemical treatments. The backbone of the glycan was a monoantennary complex-type free-N-glycan containing β1,4-branch. The pentose residue was attached to the antennal GlcNAc and released by α1,3/4-L-fucosidase. Intriguingly, the pentose residue was consistent with D-arabinose. Collectively, this glycan structure was determined to be Galβ1-4(D-Araβ1-3)GlcNAcβ1-4Manα1-3Manβ1-4GlcNAc-PA. Elevation of D-arabinose-containing free-glycans in the urine of cancer patients was confirmed by selected reaction monitoring. This is the first study to unequivocally show the occurrence of a D-arabinose-containing oligosaccharide in human together with its detailed structure.
Efficient hydrogen evolution from water using CdTe photocathodes under simulated sunlight (2017)

CdTe-based photocathodes have shown an extremely high incident photon-to-current conversion efficiency (IPCEs) of &gt;95% at 560–660 nm with an applied potential of 0 V<sub>RHE</sub>.
P177 EFFECTS OF PRE-OPERATIVE USE OF BIOLOGIC AGENTS ON INTRA-OPERATIVE BLOOD LOSS, OPERATIVE TIME AND LENGTH OF SMALL BOWEL RESECTION IN CROHN’S DISEASE PATIENTS (2018)

Crohn's & Colitis Congress of pouch creation. We aimed to compare 30-day adverse event (AE) rates for pouch creation at the time of colectomy (PTC) with delayed pouch creation (DPC). Methods: Using prospectively collected data between 2011-2015 through the National Surgical Quality Improvement Program, we conducted a cohort study including subjects 18 years with a post-operative diagnosis of UC. We assessed 30-day post-operative rates of unplanned readmissions, reoperations, major and minor AEs, comparing the stage of surgery where pouch creation took place. In a sub-analysis, we assessed AEs for those undergoing a total abdominal colectomy with ileostomy (TAC). Using a modified Poisson regression model, we estimated risk ratios (RR) with 95% confidence intervals (CI) adjusting for age, sex, race, BMI, smoking, diabetes, albumin and co-morbidities. Results: Of 2,390 IPAA procedures, 1,571 were PTC and 819 were DPC. In the PTC group, 51% were on chronic immunosuppression pre-operatively, compared with 15% in the DPC group (p<0.01) (Table AE rates are in Figure1. After controlling for confounders, patients who had DPC were significantly less likely to have unplanned reoperations (RR 0.42, 95%CI 0.24-0.75), major AEs (RR 0.72, 95%CI 0.52-0.99), and minor AEs (RR 0.48, 95%CI 0.32-0.73) than PTC. There were 2,460 TAC patients; 69% were on chronic immunosuppression. Controlling for confounders, TAC had a significantly lower risk of unplanned readmissions (RR: 0.69, 95%CI 0.58-0.81), major AEs (RR: 0.68, 95%CI: 0.54-0.84) and minor AEs (RR: 0.79, 95%CI: 0.63-0.98) compared to PTC. Conclusions: Patients undergoing delayed pouch creation were at lower risk for unplanned reoperations, major and minor AEs compared with patients undergoing PTC. Immunosuppression at the time of pouch creation may be influencing post-operative outcomes. P177
Plasma-derived exosomal miR-326, a prognostic biomarker and candidate for treatment of drug resistant pediatric acute lymphoblastic leukemia (2023)

Abstract Background Acute lymphoblastic leukemia (ALL) is a cancer with high incidence rate in pediatrics and drug resistance is a major clinical concern for ALL treatment. The current study was designed to evaluate the role of exosomal miR-326 in diagnosis and treatment of children with B-ALL. Methods Exosomes were isolated from plasma samples of 30 patients and B-ALL cell lines through 2 different methods. Exosomes were then characterization, using nanoparticle tracking analysis, immunoblotting assay and electron microscopy. qRT-PCR was employed to measure the expression levels of miR-326. Exosome uptake was validated using transfection procedure. MTT assays were performed to investigate cells viability. Results qPCR showed significant increased levels of miR-326 in patients exosomes compared with non-cancer controls ( P &lt; 0.05, AUC = 0.7500). Moreover, a comparison between the sensitive and drug resistant patients revealed a prognostic value for the exosomal miR326 ( P &lt; 0.05, AUC = 0.7755). Co-culture studies on drug resistant patient primary cells and B-ALL cell lines suggested that exosomes with high miR-326 level act as vehicles for reducing cells viability. B-ALL cell line transfection with naked miR-326 mimic confirmed the aforementioned results, and fluorescence microscopy validated uptake and internalization of exosomes by target cells. Conclusions The novel introduced features of the exosomal miR-326 addresses a non-invasive, unique way of diagnosing primary drug resistance in pediatric ALL and establishes a novel therapeutic strategy for this cancer.
Table S7 from Characterizing the immune microenvironment and neoantigen landscape of Hürthle cell carcinoma to identify potential immunologic vulnerabilities (2023)

&lt;p&gt;Neopeptides (8mer) associated with INDELS in HCC&lt;/p&gt;
Microbiology of Elizabethkingia spp. isolates in hospitalized patients. (2019)

An increasing number of infections due to Elisabethkingia spp. have been observed and reported in recent years. Here we report the microbiological aspects of 13 cases with positive cultures for Elizabethkingia spp. from 1998 to 2017. Elizabethkingia isolates were identified using the Vitek 2 Compact 60 (AES software) Gram-Negative Identification test (GNI) card (bioMerieux. Marcy-l'Etoile, France). The MICs were determined using Vitek 2 and interpreted according to CLSI guidelines based on the interpretive MIC breakpoints for Acinetobacter spp. Vitek 2 susceptibility results were confirmed using the manual E-test and the colistin result was confirmed using the broth dilution method. Twelve cases were observed between 2010 and 2017 with four cases in 2017. Of the 2017 samples, three out of four isolates were obtained outside the intensive care units compared to one out of eight samples between 2010 and 2016. There was variable susceptibility to trimethoprim/sulfamethoxazole (58.3%), ciprofloxacin (41.7%), piperacillin/tazobactam and gentamicin (16.6% each), and all were resistant to colistin. There is a high rate of drug resistance and further studies to identify the source of the infection are needed to build up a profile of Elizabethkingia spp. to inform public health policy in this context.
Safety, pharmacokinetics and efficacy of factor VIIa formulated with PEGylated liposomes in haemophilia A patients with inhibitors to factor VIII – an open label, exploratory, cross‐over, phase I/II study (2010)

Recombinant activated factor VIIa (FVIIa) is a bypassing agent used to treat bleeding episodes in haemophilia patients with inhibitors to factor VIII (FVIII) and factor IX. The pharmacological effect of FVIIa is short-lived and therefore with the recommended dose of 90 μg kg(-1), a bleeding episode is treated with multiple injections. A long-acting form of FVIIa that can ensure adequate haemostasis with a single infusion, without increasing the thrombotic risk, would therefore be beneficial. PEGylated liposomes (PEGLip) have been shown to bind FVIIa and to improve haemostatic efficacy in preclinical experiments. In the present phase I/II clinical trial, we assessed the safety and efficacy of PEGLip-formulated FVIIa in severe haemophilia A patients (FVIII≤1%) with inhibitors to FVIII. Each patient received one prophylactic infusion of standard FVIIa and one prophylactic infusion of PEGLip-formulated FVIIa. The order of the infusions was randomized and the two infusions were separated by a ten-day washout period. Efficacy assessed by thromboelastography revealed that PEGLip-FVIIa induced significantly shorter clotting times and produced higher clot firmnesses than standard FVIIa. Thrombin generation assays showed that PEGLip-FVIIa induced faster thrombin generation and higher peak levels of thrombin than standard FVIIa. These effects lasted up to 5 h postinfusion. Measurements of D-dimer, prothrombin fragment 1+2 and fibrinogen showed no significant differences between the PEGLip-FVIIa and standard FVIIa treatments. PEGLip-FVIIa therefore showed improved haemostatic efficacy without increased risk of thrombosis and may be further developed for the treatment for bleeding episodes in haemophilia patients with inhibitors.
A study of the electrical performances of isolation structures (1990)

The electrical properties of field oxide isolation structures are investigated from the device physics point of view. The importance of the potential barrier formation mechanism is clearly demonstrated through the derivation of an analytical formulation of the subthreshold current. The current independence on the isolation device length is clearly established. A large range of ideal field oxide geometries is systematically characterized to demonstrate the effect of two key parameters: the amount of buried oxide and the bird's-beak slope. The predicted isolation performances are verified on semirecessed and fully recessed structures by means of process/device simulations and experimental data. Good agreement is found between measured and calculated subthreshold currents.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prognostic value of automated KI67 scoring in breast cancer: a centralised evaluation of 8088 patients from 10 study groups (2016)

Findings from this large-scale multicentre analysis with centrally generated automated KI67 scores show strong evidence in support of a prognostic value for automated KI67 scoring in breast cancer. Given the advantages of automated scoring in terms of its potential for standardisation, reproducibility and throughput, automated methods appear to be promising alternatives to visual scoring for KI67 assessment.
Extended three-dimensional digital image correlation (X3D-DIC) (2008)

A correlation algorithm is proposed to measure full three-dimensional displacement fields in a three-dimensional domain. The chosen kinematic basis for this measurement is based on continuous finite-element shape functions. It is furthermore proposed to account for the presence of strong discontinuities, similarly to extended finite element schemes, with a suited enrichment of the kinematics with discontinuities supported by a (crack) surface. An optimization of the surface geometry is proposed based on correlation residuals. The procedure is applied to analyze one loading cycle of a fatigue-cracked nodular graphite cast iron sample by using computed tomography pictures. Subvoxel crack openings are revealed and measured.
GOTREES: PREDICTING GO ASSOCIATIONS FROM PROTEIN DOMAIN COMPOSITION USING DECISION TREES (2004)

The Gene Ontology (GO) offers a comprehensive and standardized way to describe a protein's biological role. Proteins are annotated with GO terms based on direct or indirect experimental evidence. Term assignments are also inferred from homology and literature mining. Regardless of the type of evidence used, GO assignments are manually curated or electronic. Unfortunately, manual curation cannot keep pace with the data, available from publications and various large experimental datasets. Automated literature-based annotation methods have been developed in order to speed up the annotation. However, they only apply to proteins that have been experimentally investigated or have close homologs with sufficient and consistent annotation. One of the homology-based electronic methods for GO annotation is provided by the InterPro database. The InterPro2GO/PFAM2GO associates individual protein domains with GO terms and thus can be used to annotate the less studied proteins. However, protein classification via a single functional domain demands stringency to avoid large number of false positives. This work broadens the basic approach. We model proteins via their entire functional domain content and train individual decision tree classifiers for each GO term using known protein assignments. We demonstrate that our approach is sensitive, specific and precise, as well as fairly robust to sparse data. We have found that our method is more sensitive when compared to the InterPro2GO performance and suffers only some precision decrease. In comparison to the InterPro2GO we have improved the sensitivity by 22%, 27% and 50% for Molecular Function, Biological Process and Cellular GO terms respectively.
The Definition of Transcription Units for mRNA (1978)

The detailed analysis of TUs with purified Ad2 DNA and the analysis of TU size for the bulk HeLa cell hnRNA compared to the size of mRNA of infected and uninfected cells supports the conclusion that mRNA in mammalian cells is generally derived by the processing of primary transcripts. In the context of this volume, these results indicate that the RNA transcription products of chromatin which are related to mRNA are longer than the mRNA itself. Proper functioning of chromatin in vitro must eventually take these results into account.
MO-DE-207B-06: Computer-Aided Diagnosis of Breast Ultrasound Images Using Transfer Learning From Deep Convolutional Neural Networks (2016)

Purpose: To assess the performance of using transferred features from pre-trained deep convolutional networks (CNNs) in the task of classifying cancer in breast ultrasound images, and to compare this method of transfer learning with previous methods involving human-designed features. Methods: A breast ultrasound dataset consisting of 1125 cases and 2393 regions of interest (ROIs) was used. Each ROI was labeled as cystic, benign, or malignant. Features were extracted from each ROI using pre-trained CNNs and used to train support vector machine (SVM) classifiers in the tasks of distinguishing non-malignant (benign+cystic) vs malignant lesions and benign vs malignant lesions. For a baseline comparison, classifiers were also trained on prior analytically-extracted tumor features. Five-fold cross-validation (by case) was conducted with the area under the receiver operating characteristic curve (AUC) as the performance metric. Results: Classifiers trained on CNN-extracted features were comparable to classifiers trained on human-designed features. In the non-malignant vs malignant task, both the SVM trained on CNN-extracted features and the SVM trained on human-designed features obtained an AUC of 0.90. In the task of determining benign vs malignant, the SVM trained on CNN-extracted features obtained an AUC of 0.88, compared to the AUC of 0.85 obtained by the SVM trained on human-designed features. Conclusion: We obtained strong results using transfer learning to characterize ultrasound breast cancer images. This method allows us to directly classify a small dataset of lesions in a computationally inexpensive fashion without any manual input. Modern deep learning methods in computer vision are contingent on large datasets and vast computational resources, which are often inaccessible for clinical applications. Consequently, we believe transfer learning methods will be important for computer-aided diagnosis schemes in order to utilize advancements in deep learning and computer vision without the associated costs. This work was partially funded by NIH grant U01 CA195564 and the University of Chicago Metcalf program. M.L.G. is a stockholder in R2/Hologic, co-founder and equity holder in Quantitative Insights, and receives royalties from Hologic, GE Medical Systems, MEDIAN Technologies, Riverain Medical, Mitsubishi, and Toshiba. K.D. received royalties from Hologic.
Exploring expanded wavelength regions with solid state focal plane detectors (2000)

This dissertation research has focused on the design of two spectroscopic instruments that operate outside of the UV/visible region for the analysis of volatile organic hydrocarbons and hard-to-separate hydrocarbon mixtures. The first design was solid state near infrared spectrometer. The fast acquisition rate of the NIR spectrometer allowed the monitoring of the bromination of 1-hexene. The concentrations of 1-hexene and 1,2-dibromohexane were determined for the reaction using classical least squares. The root mean squared errors of prediction for 1-hexene and 1,2-dibromohexane concentrations were 0.01 and 0.003 M, respectively. This research project also focused on the investigation of the effects of instrumental parameters on partial least squares models by comparing the results obtained from four different spectrometers. The results indicate that instrumental parameters, such as resolution and wavelength coverage, have a larger effect on experimental results than the analysis method (NIR or Raman). The second instrument design investigated here was a vacuum ultraviolet ICP-AES which monitored the 130 to 200 nm wavelength range. Fifteen nonmetals were used to determine the quantitative characteristics of the design. All elements demonstrated detection limits in the ppb range. The most sensitive emission line in this work was the aluminum 167.079 nm line which had a detection limit of 200 ppt. A VUV atomic emission line database was developed to provide an analytical reference for future investigations. The database included the emission lines from 76 elements over the 130 to 195 nm wavelength region. Over 2200 lines were observed and reported. Over 1000 of the lines were previously unreported in the two major existing references for the VUV. This work is the first VUV reference to provide truly comparable intensities for a large number of elements. A GC-VUV-ICP-AES was developed to investigate the potential of VUV-ICP atomic emission spectroscopy to provide both quantitative and qualitative information for mixtures. Chlorine and carbon chromatograms were obtained simultaneously for volatile organic hydrocarbon (VOC) mixtures. The work showed that GC-VUV-ICP-AES has the potential of generating empirical formulas for compounds by simultaneously quantitating each element in the compound and determining their ratios.
Congenital and Perinatal Varicella Infections (2022)

Varicella-zoster virus (VZV) is a human pathogen of the α-herpesvirus family. Some fetuses infected in utero around 8-20 weeks of pregnancy show signs of congenital varicella syndrome (CVS). Infants born to mothers who develop varicella within 5 days before and 2 days after delivery can experience severe disease with increased mortality. The best diagnostic modality is polymerase chain reaction (PCR), which can be done using vesicular swabs or scrapings, scabs from crusted lesions, tissue from biopsy samples, and cerebrospinal fluid. The prevention and management of varicella infections include vaccination, anti-VZV immunoglobulin, and specific antiviral drugs. In this article, we have reviewed the characteristics of VZV, clinical manifestations, management of perinatal infections, and short- and long-term prognosis.