gebhart/patrepeval huggingface dataset:
Experience with Esophagogastrointestinal Transit Scintigraphy in the Initial 229 Patients: Multiple Regions of Dysmotility Are Common (2020)

The purpose of this investigation was to review our experience with our comprehensive esophagogastrointestinal transit study in the first 229 patients. This scintigraphic study analyzes the motility of the entire gut, from the esophagus through the rectosigmoid colon. <b>Methods:</b> Data were reviewed for our first 2 y of experience with this examination (184 women and 45 men aged 20-79 y [mean ± SD, 44 ± 16 y]). Patients were referred with symptoms suggestive of a motility disorder. They first swallowed <sup>111</sup>In-diethylenetriaminepentaacetic acid in water for the esophageal-swallow study and then 300 mL for a 30-min <sup>111</sup>In water-only study, followed by 120 mL of <sup>111</sup>In water simultaneously with the solid standardized <sup>99m</sup>Tc egg-substitute meal. Images and quantification were obtained for esophageal transit, water-only gastric emptying, water-with-solid gastric emptying, small-bowel transit, and colonic transit. <b>Results:</b> Of the 229 patient studies, 45 (20%) were normal. The remaining 184 (80%) had at least 1 region of dysmotility, for a total of 336 regions of abnormal motility. A single region of dysmotility was seen in 92 patients (50%), 2 regions in 50 (27%), 3 regions in 26 (14%), 4 regions in 12 (7%), and 5 regions in 4 (2%). There was a poor correlation between the results of the water-only study and water with the solid meal. Three different patterns of delayed colonic transit were seen. Patient symptoms were often not predictive of the scintigraphic findings. <b>Conclusion:</b> This study highlights the frequent occurrence of dysmotility in more than 1 region of the gastrointestinal tract in patients with a suspected motility disorder and the frequent concurrence of both upper- and lower-tract dysmotility in the same patients. It provides information to referring physicians regarding which motility disorders may be causing the patient symptoms, why the patient is or is not responding to the present therapy, and if and what additional workup and therapy may be needed.
Argonne Intense Pulsed Neutron Source Used to Solve the Molecular Structure of a Novel Organometallic Complex (1983)

The single-crystal structure of Mn(CO)(3)(C(7)H(11)) is the first to be solved by direct methods based on time-of-flight neutron diffraction data obtained at the Argonne Intense Pulsed Neutron Source. The molecule contains an unusual three-center, two-electron manganese-hydrogen-carbon interaction.
Inclusion of Endogenous Plasma Dehydroepiandrosterone Sulfate and Mammographic Density in Risk Prediction Models for Breast Cancer (2020)

Combining DHEAS and mammographic density could help identify women at high risk who may benefit from individualized breast cancer screening and/or preventive measures among postmenopausal women.
On Separation for Multiple Access Channels (2006)

We examine the issue of separation for multiple access channels.We demonstrate that source-channel separation holds for noisy multiple access channels, when the channel operates over a common finite field.This robustness of separation is predicated on the fact that noise and inputs are independent, and we examine the loss from failure of separation when noise is input dependent.
Action potential detection with automatic template matching (2005)

Detecting action potentials has an important role in analyzing extracellular neuronal recordings. Current algorithms require subjective tuning by a user in the form of user-specified parameters. This work describes a fully automatic template-matching spike detection algorithm that does not require any tuning. This algorithm is robust to noise and performs better than an optimum threshold detection algorithm.
Non-collisional heating in inductively coupled plasma sources (2002)

Summary form only given. In inductively coupled plasma (ICP) reactors for microelectronics fabrication, the plasma is sustained by an electromagnetic (EM) wave generated by an external antenna. In models of radio frequency (rf) ICP reactors, the charged particle transport is addressed using a variety of methods including fluid, kinetic or Monte Carlo (MC) techniques. The plasma dynamics are usually coupled back to the EM wave through Ohm's law, which relates the electric field to the plasma current. Ohm's law, which only considers collisional heating, is strictly accurate only when the electron collision frequency is commensurate or greater than the rf frequency. Previous studies have suggested that additional heating mechanisms are present at lower gas pressures (<10-20 mTorr) in the reactors of interest. In this paper, we report on a new algorithm whose intent is to a provide more accurate description of non-collisional plasma-EM wave coupling at low pressures in ICP reactors where ohmic heating may not be strictly applicable. The algorithm is implemented in a 2-dimensional model for an ICP plasma etching reactor.
Power loop busbars design and experimental validation of 1 kV, 5 kA Solid State Circuit Breaker using parallel connected RB-IGCTs (2020)

This paper investigates the design of 1 kV, 5 kA solid state circuit breaker by using parallel connection of Reverse Blocking IGCTs (RB-IGCT). The presented breaker topology is based on the parallel connection of low conduction loss RB-IGCTs which delivers efficiency as high as 99.9%. The focus of this paper is on the power loop design and experimental validation of parallel connection of two and three RB-IGCTs with emphasis on current sharing during dynamic events such as short-circuits. A 3D-CAD based design of power loop busbars was verified by several simulation test cases to represent dynamic current sharing under variations in RB-IGCT package impedances. The experimental results confirm that the parallel topology is able to perform current interruption during overload and short-circuit situations up to 10 kA for two devices in parallel and up to 14 kA for three devices in parallel - with current deviation from the mean as little as 6%.
Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and Virulence (2016)

The opportunistic fungal pathogen Cryptococcus neoformans is a major cause of mortality in immunocompromised individuals, resulting in more than 600,000 deaths per year. Many human fungal pathogens secrete peptidases that influence virulence, but in most cases the substrate specificity and regulation of these enzymes remains poorly understood. The paucity of such information is a roadblock to our understanding of the biological functions of peptidases and whether or not these enzymes are viable therapeutic targets. We report here an unbiased analysis of secreted peptidase activity and specificity in C. neoformans using a mass spectrometry-based substrate profiling strategy and subsequent functional investigations. Our initial studies revealed that global peptidase activity and specificity are dramatically altered by environmental conditions. To uncover the substrate preferences of individual enzymes and interrogate their biological functions, we constructed and profiled a ten-member gene deletion collection of candidate secreted peptidases. Through this deletion approach, we characterized the substrate specificity of three peptidases within the context of the C. neoformans secretome, including an enzyme known to be important for fungal entry into the brain. We selected a previously uncharacterized peptidase, which we term Major aspartyl peptidase 1 (May1), for detailed study due to its substantial contribution to extracellular proteolytic activity. Based on the preference of May1 for proteolysis between hydrophobic amino acids, we screened a focused library of aspartyl peptidase inhibitors and identified four high-affinity antagonists. Finally, we tested may1Δ strains in a mouse model of C. neoformans infection and found that strains lacking this enzyme are significantly attenuated for virulence. Our study reveals the secreted peptidase activity and specificity of an important human fungal pathogen, identifies responsible enzymes through genetic tests of their function, and demonstrates how this information can guide the development of high affinity small molecule inhibitors.
Editor’s Highlight: Pregnancy Alters Aflatoxin B1 Metabolism and Increases DNA Damage in Mouse Liver (2017)

Pregnancy is a complex physiological state, in which the metabolism of endogenous as well as exogenous agents is ostensibly altered. One exogenous agent of concern is the hepatocarcinogen aflatoxin B1 (AFB1), a foodborne fungal toxin, that requires phase I metabolic oxidation for conversion to its toxic and carcinogenic form, the AFB1-8,9-exo-epoxide. The epoxide interacts with cellular targets causing toxicity and cell death; these targets include the covalent modification of DNA leading to mutations that can initiate malignant transformation. The main detoxification pathway of the AFB1-epoxide involves phase II metabolic enzymes including the glutathione-S-transferase (GST) family. Pregnancy can modulate both phase I and II metabolism and alter the biological potency of AFB1. The present work investigated the impact of pregnancy on AFB1 exposure in mice. A single IP dose of 6 mg/kg AFB1 was administered to pregnant C57BL/6 J mice at gestation day 14 and matched non-pregnant controls. Pregnant mice accumulated 2-fold higher AFB1-N7-guanine DNA adducts in the liver when compared with nonpregnant controls 6 h post-exposure. Enhanced DNA adduct formation in pregnant animals paralleled elevated hepatic protein expression of mouse CYP1A2 and mouse homologs of human CYP3A4, phase I enzymes capable of bioactivating AFB1. Although phase II enzymes GSTA1/2 showed decreased protein expression, GSTA3, the primary enzymatic protection against the AFB1-epoxide, was unaffected at the protein level. Taken together, our results reveal that pregnancy may constitute a critical window of susceptibility for maternal health, and provide insight into the biochemical factors that could explain the underlying risks.
Inferring relations and individuals relevant to a situation: An example (2014)

In various scenarios, agents need to exchange information about situations - either the situations they are currently in or in reference to other circumstances. Assuming that agents are intelligent agents, i.e., they have their own inference capabilities, the question then is - which parts of the knowledge that an agent has need to be sent over (possibly narrow bandwidth) communication links in order to provide a complete description of the situation? Or in other words, which part of the agent's knowledge is relevant to a specific situation? The assumption behind this question is that only a small part of the agent's knowledge needs to be sent since the receiving agent can infer the rest of it locally. This paper discusses an example of reasoning about the relevancy of information. First, the notion of relevancy is defined. Then an implementation of relevance inference scenario is described.
Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate (2016)

Alkyl branching at the β position of a polyketide intermediate is an important variation on canonical polyketide natural product biosynthesis. The branching enzyme, 3-hydroxy-3-methylglutaryl synthase (HMGS), catalyzes the aldol addition of an acyl donor to a β-keto-polyketide intermediate acceptor. HMGS is highly selective for two specialized acyl carrier proteins (ACPs) that deliver the donor and acceptor substrates. The HMGS from the curacin A biosynthetic pathway (CurD) was examined to establish the basis for ACP selectivity. The donor ACP (CurB) had high affinity for the enzyme (Kd = 0.5 μM) and could not be substituted by the acceptor ACP. High-resolution crystal structures of HMGS alone and in complex with its donor ACP reveal a tight interaction that depends on exquisite surface shape and charge complementarity between the proteins. Selectivity is explained by HMGS binding to an unusual surface cleft on the donor ACP, in a manner that would exclude the acceptor ACP. Within the active site, HMGS discriminates between pre- and postreaction states of the donor ACP. The free phosphopantetheine (Ppant) cofactor of ACP occupies a conserved pocket that excludes the acetyl-Ppant substrate. In comparison with HMG-CoA (CoA) synthase, the homologous enzyme from primary metabolism, HMGS has several differences at the active site entrance, including a flexible-loop insertion, which may account for the specificity of one enzyme for substrates delivered by ACP and the other by CoA.
Within-Host Evolution Results in Antigenically Distinct GII.4 Noroviruses (2014)

Noroviruses are agents of gastrointestinal illness, infecting an estimated 21 million people per year in the United States alone. In healthy individuals, symptomatic infection typically resolves within 24 to 48 h. However, symptoms may persist for years in immunocompromised individuals, and development of successful treatments for these patients is a continuing challenge. This work is relevant to the design of successful norovirus therapeutics for chronically infected patients; provides support for previous assertions that chronically infected individuals may serve as reservoirs for new, antigenically unique emergent strains; and furthers our understanding of genogroup II, genotype 4 (GII.4) norovirus immune-driven molecular evolution.
Analysis of Stress Responsive Genes Induced by Single-Walled Carbon Nanotubes in BJ Foreskin Cells (2007)

Nanotechnology is finding its use as a potential technology in consumer products, defense, electronics, and medical applications by exploiting the properties of nanomaterials. Single-walled carbon nanotubes are novel forms of these nanomaterials with potential for large applications. However, the toxicity studies on this material are not explored in detail and therefore limiting its use. It has been earlier reported that single-walled carbon nanotubes induces oxidative stress and also dictates activation of specific signaling pathway in keratinocytes. The present study explores the effect of single-walled carbon nanotubes on stress genes in human BJ Foreskin cells. The results show induction of oxidative stress in BJ Foreskin cells by single-walled carbon nanotubes and increase in stress responsive genes. The genes included inducible genes like HMOX1, HMOX2, and Cyp1B1. In addition we validated increase for four genes by SWCNT, namely ATM, CCNC, DNAJB4, and GADD45A by RT-PCR. Moreover results of the altered stress related genes have been discussed and that partially explains some of the toxic responses induced by single-walled carbon nanotubes.
Analysis of Retinal Architectural Changes Using Intraoperative OCT Following Surgical Manipulations With Membrane Flex Loop in the DISCOVER Study (2017)

Acute retinal alterations after ILM peeling with the membrane flex loop were visualized at a frequency of less than 10%. Additional research is needed to understand the clinical impact, if any, of these architectural alterations.
MLVA fingerprinting of Brucella melitensis circulating among livestock and cases of sporadic human illness in Egypt (2020)

Brucella melitensis is a serious public health threat, with human infection exhibiting acute febrile illness and chronic health problems. The present study investigated the genetic diversity and epidemiological links of the important zoonotic bacterium B. melitensis in Egypt using multilocus variable-number tandem repeat analysis (MLVA-16) including eight minisatellite (panel 1) and eight microsatellite (panel 2, subdivided into 2A and 2B) markers. A total of 118 isolates were identified as B. melitensis biovar 3 by classical biotyping and Bruce-ladder assay. Although B. melitensis is primarily associated with infection in sheep and goats, most of B. melitensis isolates in this study were obtained from secondary hosts (cattle, buffaloes, humans and a camel) suggesting cross-species adaptation of B. melitensis to large ruminants in Egypt. The MLVA-16 scheme competently discriminated 70 genotypes, with 51 genotypes represented by single isolates, and the remaining 19 genotypes were shared among 67 isolates, suggesting both sporadic and epidemiologically related characteristics of B. melitensis infection. Matching of local genotypes with representatives of global genotypes revealed that the majority of Egyptian isolates analysed had a West Mediterranean descendance. As this study represents the first comprehensive genotyping and genetic analysis of B. melitensis from different sources in Egypt, the information generated from this study will augment knowledge about the main epidemiological links associated with this bacterium and will allow a better understanding of the current epidemiological situation of brucellosis in Egypt. Ultimately, this will help to adopt effective brucellosis intervention strategies in Egypt and other developing nations.
Will There Be a Cure for Ebola? (2016)

Despite the unprecedented Ebola virus outbreak response in West Africa, no Ebola medical countermeasures have been approved by the US Food and Drug Administration. However, multiple valuable lessons have been learned about the conduct of clinical research in a resource-poor, high risk-pathogen setting. Numerous therapeutics were explored or developed during the outbreak, including repurposed drugs, nucleoside and nucleotide analogues (BCX4430, brincidofovir, favipiravir, and GS-5734), nucleic acid-based drugs (TKM-Ebola and AVI-7537), and immunotherapeutics (convalescent plasma and ZMapp). We review Ebola therapeutics progress in the aftermath of the West Africa Ebola virus outbreak and attempt to offer a glimpse of a path forward.
A piezomodulated reflectance study of InAs/GaAs surface quantum dots (2006)

Piezomodulated reflectance (PzR) spectra have been measured for two samples of InAs surface quantum dots (SQDs) deposited on GaAs (311)B substrates with In0.35Ga0.65As template. At 77K multiple confined-state SQDs transitions can be clearly resolved from the PzR spectra . The detailed optical transition features of SQDs, QDs buried by capping layer, In0.35Ga0.65As template and GaAs substrate layers were obtained from well-fitted PzR spectra using the first or third derivative of a Lorentz line shape. Differences between PzR results of two samples were discussed qualitatively.
P097: The status quo of involved-field radiotherapy – Quality analysis of radiotherapy in the GHSG HD 16 (2022)

Question: The HD 16 trial of the German Hodgkin Study Group (GHSG) investigated the use of consolidative radiotherapy (RT) after 2 cycles of ABVD chemotherapy for early-stage Hodgkin lymphoma (HL) and could demonstrate the superiority of a combined modality approach [1]. The present work aims at analyzing the quality of involved-field RT used in this study. Methods/Material: For quality assessment, 100 randomly chosen plans from the HD 16 trial were requested and analyzed. RT was assessed by experts of the radiation therapy panel of the GHSG using initial (staging) imaging, RT plans and the recommendation forms by the reference radiation oncology. Evaluation was graded as „correct“, „minor deviation“ or „major deviation“. Statistical analyses were performed using SPSS (version 27/28, IBM, NY, USA). Results: Radiation doses were adequate with a median of 20 Gy (19.8 Gy-21.6 Gy) in normofractionation. In the majority of radiation series, supradiaphragmatic target volumes were treated (91 %), with the regions most commonly irradiated being supraclavicular left/right (73 % each), infraclavicular left/right (73 % each) and cervical left/right (44 % and 45 %, respectively). Acute treatment toxicities were mild to moderate with only 3 cases of grade 3–4 toxicities (1 nausea/vomiting, 1 dysphagia, 1 mucositis). According to the RT panel, 84 % of cases were evaluated as „correct“, 5 % as „minor deviations“ and 11 % as „major deviations“. Major deviations were caused by insufficient dose coverage of involved regions in most cases (10/11), predominantly in the upper mediastinum (5/10 cases). Previous GHSG studies in early-stage HL (HD 10 [2] and HD 13 [3]) showed lower rates of RT series according to protocol (38.8 % and 52 %, respectively). A χ2-test was used to compare the number of correct RT series in the different GHSG study generations (HD 13 vs. HD 16). No expected cell frequencies were below 5. Results reveal a significant improvement in favor of HD 16 (χ2(1)=33.8, p<0.001 Φ=-0.247). Similar outcomes were found for the association of GHSG study generation and the absence of major deviations (χ2(1)=27.4, p<0.001 Φ=- 0.222). Conclusion: Since its introduction in HD10, involved-field RT has evolved considerably. However, continuous efforts in RT quality assurance and training are needed in the modern era. Literature 1.JCO. November 2019; 37(31):2835-2845. 2.IJROBP. August 2008; 71 (5):1419-1424. 3.SUON. February 2017;193(2):109-115.
Brain-Computer Interface Based on Generation of Visual Images (2011)

This paper examines the task of recognizing EEG patterns that correspond to performing three mental tasks: relaxation and imagining of two types of pictures: faces and houses. The experiments were performed using two EEG headsets: BrainProducts ActiCap and Emotiv EPOC. The Emotiv headset becomes widely used in consumer BCI application allowing for conducting large-scale EEG experiments in the future. Since classification accuracy significantly exceeded the level of random classification during the first three days of the experiment with EPOC headset, a control experiment was performed on the fourth day using ActiCap. The control experiment has shown that utilization of high-quality research equipment can enhance classification accuracy (up to 68% in some subjects) and that the accuracy is independent of the presence of EEG artifacts related to blinking and eye movement. This study also shows that computationally-inexpensive bayesian classifier based on covariance matrix analysis yields similar classification accuracy in this problem as a more sophisticated Multi-class Common Spatial Patterns (MCSP) classifier.
Inhibitors of the Cancer Target Ribonucleotide Reductase, Past and Present (2022)

Ribonucleotide reductase (RR) is an essential multi-subunit enzyme found in all living organisms; it catalyzes the rate-limiting step in dNTP synthesis, namely, the conversion of ribonucleoside diphosphates to deoxyribonucleoside diphosphates. As expression levels of human RR (hRR) are high during cell replication, hRR has long been considered an attractive drug target for a range of proliferative diseases, including cancer. While there are many excellent reviews regarding the structure, function, and clinical importance of hRR, recent years have seen an increase in novel approaches to inhibiting hRR that merit an updated discussion of the existing inhibitors and strategies to target this enzyme. In this review, we discuss the mechanisms and clinical applications of classic nucleoside analog inhibitors of hRRM1 (large catalytic subunit), including gemcitabine and clofarabine, as well as inhibitors of the hRRM2 (free radical housing small subunit), including triapine and hydroxyurea. Additionally, we discuss novel approaches to targeting RR and the discovery of new classes of hRR inhibitors.