gebhart/patrepeval huggingface dataset:
A Chemical Method for Labeling Lysine Methyltransferase Substrates (2010)

Several protein lysine methyltransferases (PKMTs) modify histones to regulate chromatin-dependent cellular processes, such as transcription, DNA replication and DNA damage repair. PKMTs are likely to have many additional substrates in addition to histones, but relatively few nonhistone substrates have been characterized, and the substrate specificity for many PKMTs has yet to be defined. Thus, new unbiased methods are needed to find PKMT substrates. Here, we describe a chemical biology approach for unbiased, proteome-wide identification of novel PKMT substrates. Our strategy makes use of an alkyne-bearing S-adenosylmethionine (SAM) analogue, which is accepted by the PKMT, SETDB1, as a cofactor, resulting in the enzymatic attachment of a terminal alkyne to its substrate. Such labeled proteins can then be treated with azide-functionalized probes to ligate affinity handles or fluorophores to the PKMT substrates. As a proof-of-concept, we have used SETDB1 to transfer the alkyne moiety from the SAM analogue onto a recombinant histone H3 substrate. We anticipate that this chemical method will find broad use in epigenetics to enable unbiased searches for new PKMT substrates by using recombinant enzymes and unnatural SAM cofactors to label and purify many substrates simultaneously from complex organelle or cell extracts.
31. Tetragtdrfuran Complexes of Selected Early Transition Metals. (1982)

This chapter contains sections titled: Tetrachlorobis(tetrahydrofurn)titanium(IV),TiCl4(thf)2 Tetrachlorobis(tetrahydrofurn)zirconium(IV),ZrCl4(thf)2 Tetrachlorobis(tetrahydrofurn)hafnium(IV),HfCl4(thf)2 Tetrachlorobis(tetrahydrofurn)titanium(III),TiCl3(thf)3 Tetrachlorobis(tetrahydrofurn)vanadium(III),VCl3(thf)3 Tetrachlorobis(tetrahydrofurn)niobium(IV),NbCl4(thf)2 Tetrachlorobis(tetrahydrofurn)scandium(III),ScCl3(thf)3
Restoration of Scanning Tunneling Microscope Images by means of Two-Dimensional Maximum Entropy Method (2002)

We present a new technique for the restoration of scanning tunneling microscopy (STM) images, which is a two-dimensional extension of a recently developed statistical approach based on the one-dimensional least-squares method (LSM). An STM image is regarded as a realization of a stochastic process and assumed to be a composition of an underlying image and noise. We express the underlying image in terms of a two-dimensional generalized trigonometric polynomial suitable for representing the atomic protrusions in STM images. The optimization of the polynomial is performed by the two-dimensional LSM combined with the power spectral density function estimated by means of the maximum entropy method (MEM) iterative algorithm for two-dimensional signals. The restored images are obtained as the optimum least-squares fitting polynomial which is a continuous surface. We apply this technique to modeled and actual STM data. Results show that the present method yields a reasonable restoration of STM images.
A Clinical Trial Based on Reward Contingency to Improve Prone Tolerance and Motor Development is Feasible in 3- to 6-Month-Old Infants (2020)

Aims : The American Academy of Pediatrics recommends “parents to incorporate supervised, awake ‘prone play’ in their infant’s routine to support motor development and minimize the risk of plagiocephaly”. The purpose of this feasibility study was to compare usual care to a reward contingency–based intervention, developed to increase prone tolerance and improve motor skills. Methods : Ten full-term infants, 3–6- months old, with poor prone tolerance were randomized to either the Education group or Reward contingency group. Each group participated in three parent education sessions and 15 intervention sessions, over the period of three weeks. Infants in the Reward contingency group used the Prone Play Activity Center, a technology developed to reinforce motor behavior of infants in prone position. Intervention frequency and parent feedback data determined the feasibility of the interventions. Results : Infants in the Reward contingency group practiced a median of 12 of the 15 anticipated intervention sessions in the Prone Play Activity Center. These infants used the device for a mean of 18 minutes per day. Parents of infants in the Education group practiced a median of 10 sessions of the 15 anticipated intervention sessions. Conclusion : The reward contingency–based intervention is feasible for use in a future clinical trial with some modifications.
AirCode (2017)

We present AirCode, a technique that allows the user to tag physically fabricated objects with given information. An AirCode tag consists of a group of carefully designed air pockets placed beneath the object surface. These air pockets are easily produced during the fabrication process of the object, without any additional material or postprocessing. Meanwhile, the air pockets affect only the scattering light transport under the surface, and thus are hard to notice to our naked eyes. But, by using a computational imaging method, the tags become detectable. We present a tool that automates the design of air pockets for the user to encode information. AirCode system also allows the user to retrieve the information from captured images via a robust decoding algorithm. We demonstrate our tagging technique with applications for metadata embedding, robotic grasping, as well as conveying object affordances.
Faculty Opinions recommendation of A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. (2013)

Among bacterial toxin/antitoxin (TA) systems, to date no antitoxin has been identified that functions by cleaving toxin mRNA. Here we demonstrate YjdO (renamed GhoT) is a membrane lytic peptide that causes ghost cell formation (lysed cells with damaged membranes) and increases persistence (persister cells are tolerant to antibiotics without undergoing genetic change). GhoT is part of a novel TA system with YjdK (renamed GhoS) since in vitro RNA degradation studies, qRT-PCR, and whole-transcriptome studies revealed GhoS masks GhoT toxicity by cleaving specifically ghoT mRNA. Alanine substitutions showed arginine 28 is important for GhoS activity, and RNA sequencing indicated the GhoS cleavage site is rich in uridine and adenosine.
Benchmarking ChatGPT-4 on ACR Radiation Oncology In-Training (TXIT) Exam and Red Journal Gray Zone Cases: Potentials and Challenges for AI-Assisted Medical Education and Decision Making in Radiation Oncology (2023)

The potential of large language models in medicine for education and decision making purposes has been demonstrated as they achieve decent scores on medical exams such as the United States Medical Licensing Exam (USMLE) and the MedQA exam. In this work, we evaluate the performance of ChatGPT-4 in the specialized field of radiation oncology using the 38th American College of Radiology (ACR) radiation oncology in-training (TXIT) exam and the 2022 Red Journal Gray Zone cases. For the TXIT exam, ChatGPT-3.5 and ChatGPT-4 have achieved the scores of 63.65% and 74.57%, respectively, highlighting the advantage of the latest ChatGPT-4 model. Based on the TXIT exam, ChatGPT-4's strong and weak areas in radiation oncology are identified to some extent. Specifically, ChatGPT-4 demonstrates better knowledge of statistics, CNS &amp; eye, pediatrics, biology, and physics than knowledge of bone &amp; soft tissue and gynecology, as per the ACR knowledge domain. Regarding clinical care paths, ChatGPT-4 performs better in diagnosis, prognosis, and toxicity than brachytherapy and dosimetry. It lacks proficiency in in-depth details of clinical trials. For the Gray Zone cases, ChatGPT-4 is able to suggest a personalized treatment approach to each case with high correctness and comprehensiveness. Importantly, it provides novel treatment aspects for many cases, which are not suggested by any human experts. Both evaluations demonstrate the potential of ChatGPT-4 in medical education for the general public and cancer patients, as well as the potential to aid clinical decision-making, while acknowledging its limitations in certain domains. Because of the risk of hallucination, facts provided by ChatGPT always need to be verified.
Controllable reductive method for synthesizing metal-containing particles (2023)

The invention is directed to a method for producing metal-containing particles, the method comprising subjecting an aqueous solution comprising a metal salt, E.sub.h, lowering reducing agent, pH adjusting agent, and water to conditions that maintain the E.sub.h value of the solution within the bounds of an E.sub.h-pH stability field corresponding to the composition of the metal-containing particles to be produced, and producing said metal-containing particles in said aqueous solution at a selected E.sub.h value within the bounds of said E.sub.h-pH stability field. The invention is also directed to the resulting metal-containing particles as well as devices in which they are incorporated.
GDF15 is elevated in mice following retinal ganglion cell death and in glaucoma patients (2017)

Glaucoma is the second leading cause of blindness worldwide. Physicians often use surrogate endpoints to monitor the progression of glaucomatous neurodegeneration. These approaches are limited in their ability to quantify disease severity and progression due to inherent subjectivity, unreliability, and limitations of normative databases. Therefore, there is a critical need to identify specific molecular markers that predict or measure glaucomatous neurodegeneration. Here, we demonstrate that growth differentiation factor 15 (GDF15) is associated with retinal ganglion cell death. Gdf15 expression in the retina is specifically increased after acute injury to retinal ganglion cell axons and in a murine chronic glaucoma model. We also demonstrate that the ganglion cell layer may be one of the sources of secreted GDF15 and that GDF15 diffuses to and can be detected in aqueous humor (AH). In validating these findings in human patients with glaucoma, we find not only that GDF15 is increased in AH of patients with primary open angle glaucoma (POAG), but also that elevated GDF15 levels are significantly associated with worse functional outcomes in glaucoma patients, as measured by visual field testing. Thus, GDF15 maybe a reliable metric of glaucomatous neurodegeneration, although further prospective validation studies will be necessary to determine if GDF15 can be used in clinical practice.
Chylous Ascites in a Patient With Mesenteric Panniculits (2008)

Rush University Medical Center and Adult Care Specialists, 1538 N Arlington Heights Road, Arlington Heights, IL The authors declare no conflict of interest. The authors confirm that there is no financial interests or affiliations with institutions, organizations, or companies that are mentioned in the manuscript or whose products or services discussed. There is no support for the report from any manufacturer of drug, appliance, or treatment or its competitor.
Achievable uplink rates for massive MIMO with coarse quantization (2017)

The high hardware complexity of a massive MIMO base station, which requires hundreds of radio chains, makes it challenging to build commercially. One way to reduce the hardware complexity and power consumption of the receiver is to lower the resolution of the analog-to-digital converters (ADCs). We derive an achievable rate for a massive MIMO system with arbitrary quantization and use this rate to show that ADCs with as low as 3 bits can be used without significant performance loss at spectral efficiencies around 3.5 bpcu per user, also under interference from stronger transmitters and with some imperfections in the automatic gain control.
Performance study of the CMS barrel resistive plate chambers with cosmic rays (2010)

In October and November 2008, the CMS collaboration conducted a programme of&#13;\ncosmic ray data taking, which has recorded about 270 million events. The Resistive Plate Chamber&#13;\nsystem, which is part of the CMS muon detection system, was successfully operated in the full&#13;\nbarrel. More than 98% of the channels were operational during the exercise with typical detection&#13;\nefficiency of 90%. In this paper, the performance of the detector during these dedicated runs is&#13;\nreported.
High-risk localised prostate cancer: multimodal treatment strategies combining neoadjuvant hormonal therapy and/or chemotherapy with radical prostatectomy (2003)

For patients with newly diagnosed prostate cancer, clinical tumour stage, Gleason score of the diagnostic biopsy specimen and serum prostate-specific antigen (PSA) level can be combined to identify a group of men at increased risk of treatment failure after radiotherapy or radical prostatectomy. For these high-risk, but still clinically localised prostate cancers, multimodal treatment strategies may result in improved cancer control outcomes. Indeed, in the setting of clinical stage T3 – T4 tumours, the combination of radiotherapy followed by hormonal therapy has improved patient survival. The benefits of adjuvant or neoadjuvant hormonal and/or chemotherapy followed by radical prostatectomy in this setting are unclear, but are the subject of ongoing or planned Phase III clinical trials. These studies will help define the role of multimodal treatment strategies in this high-risk patient population.
Platform for Accurate Efficiency Quantification of > 35% Efficient Thermophotovoltaic Cells (2021)

Thermophotovoltaic (TPV) devices convert thermal radiation directly into electricity using semiconductor diodes and have a variety of uses from waste heat recovery to energy storage to primary power conversion. Recent results have demonstrated promising cells nearing and surpassing 30% conversion efficiency. As TPV cells continue to increase in efficiency, they become attractive for a wider range of applications. Their efficiencies must be quantified in a standardized fashion to compare results accurately across research groups. Here, we outline and quantify the most important characteristics of an accurate and precise TPV efficiency measurement. Using a custom-built measurement apparatus that takes these characteristics into account, we report 19 cells with greater than 30% conversion efficiency and 2 cells with greater than 35% conversion efficiency. This confirms that our reported cell efficiencies are not simply those of hero cells but rather of a distribution of cells that can be produced in a consistent, high-quality process.
Viral and bacterial pathogens identification in children hospitalised for severe pneumonia and parapneumonic empyema (2012)

Pneumonia is caused by respiratory bacteria and/or viruses. Little is known if co-infections are an aggravating factor in hospitalised children with severe pneumonia. We studied the impact of respiratory pathogens on the severity of pneumonia. Between 2007 and 2009, 52 children hospitalised with a well-documented diagnosis of community-acquired pneumonia (CAP), with or without parapneumonic empyema (PPE), were enrolled in the study. The patients were classified into 2 groups: CAP + PPE (<i>n</i> = 28) and CAP (<i>n</i> = 24). The identification of respiratory viruses and bacteria in nasopharyngeal aspirates and pleural effusion samples were performed using conventional bacterial techniques and molecular assays. Using real-time multiplex PCR and antigen detection, <i>Streptococcus pneumoniae</i> was the main agent identified in 76% of the cases by molecular tests and BinaxNOW® in pleural fluid. A total of 8% of pleural fluid samples remained undiagnosed. In nasopharyngeal aspirates, rhinovirus, parainfluenza viruses, human metapneumovirus, and respiratory syncytial virus were detected in both CAP and CAP + PPE populations; however, the percentage of viral co-detection was significantly higher in nasopharyngeal aspirates from CAP + PPE patients (35%) compared with CAP patients (5%). In conclusion, viral co-detection was observed mainly in patients with more severe pneumonia. Molecular biology assays improved the pathogens detection in pneumonia and confirmed the <i>S. pneumoniae</i> detection by BinaxNOW® in pleural effusion samples. Interestingly, the main <i>S. pneumoniae</i> serotypes found in PPE are not the ones targeted by the heptavalent pneumococcal conjugate vaccine.
Update rates constraints in fixed-panel Radar Search Pattern Optimization with limited time budget (2017)

Electronic Phased-Array Radars offer new possibilities for Radar Search Pattern Optimization by using bi-dimensional beam-forming and beam steering, along both elevation and azimuth axes. The Radar Search Pattern Optimization problem can be approximated as a Set Cover problem and solved using Integer Programming methods. This approximation can be extended to account for direction-specific scan update rates constraints without the need to modify the optimization algorithm.
Expression of the cellular oxygen sensor PHD2 (EGLN-1) predicts radiation sensitivity in squamous cell cancer of the head and neck (2009)

We found low PHD2 expression and in particular low nuclear expression to predict a favourable response to RT. Therefore, nuclear PHD2 expression may act as a surrogate marker for radiation resistance in HNSCC.
Cleveland Clinic Postural Stability Index Norms for the Balance Error Scoring System (2018)

The CC-PSI provides a quantitative, objective measure of postural stability, overcoming the limitations associated with conventional BESS scoring. Optimal concussion management should use objective age- and sex-specific values in the evaluation of postural stability. The normative values of the CC-PSI may be used in the absence of a baseline BESS evaluation to aid clinical decision making.
Bone and high-density lipoprotein: The beginning of a beautiful friendship (2016)

There is a tight link between bone and lipid metabolic pathways. In this vein, several studies focused on the exploration of high-density lipoprotein (HDL) in the pathobiology of bone diseases, with emphasis to the osteoarthritis (OA) and osteoporosis, the most common bone pathologies. Indeed, epidemiological and in vitro data have connected reduced HDL levels or dysfunctional HDL with cartilage destruction and OA development. Recent studies uncovered functional links between HDL and OA fueling the interesting hypothesis that OA could be a chronic element of the metabolic syndrome. Other studies have linked HDL to bone mineral density. Even though at epidemiological levels the results are conflicting, studies in animals as well as in vitro experiments have shown that HDL facilitates osteoblastogensis and bone synthesis and most probably affects osteoclastogenesis and osteoclast bone resorption. Notably, reduced HDL levels result in increased bone marrow adiposity affecting bone cells function. Unveiling the mechanisms that connect HDL and bone/cartilage homeostasis may contribute to the design of novel therapeutic agents for the improvement of bone and cartilage quality and thus for the treatment of related pathological conditions.
Introduction (2018)

Chapter 1 introduces the semantic and metaphysical problem raised by the expanding uses of psychological predicates throughout biology. Sellars’ widely-known framework of the Manifest and Scientific Images provides a stepping stone for initial grasp of the current anthropocentrism in interpreting psychological predicates and the capacities to which they refer. The chapter introduces Literalism, which holds that the predicates are used literally with the same reference across human and nonhuman biological domains. This view is the natural conclusion of a plausible interpretation of scientific practices and discernible trends in those practices. The chapter also provides an outline of the book, a summary of subsequent chapters, and a brief discussion of consciousness, panpsychism, and content.
A comparative X‐ray photoelectron spectroscopy and medium‐energy ion‐scattering study of ultra‐thin, Hf‐based high‐k films (2010)

Abstract Ultra‐thin high‐k layers based on HfO 2 , or Hf‐silicates in combination with sub‐nanometer SiO 2 , show much promise in their use as Si‐compatible gate dielectrics. XPS has been applied on a range of HfO 2 /SiO 2 and HfSiO x (60%Hf)/SiO 2 films on Si(100), before and after decoupled plasma nitridation (DPN) at 1073 K. The treatment of the data was optimized in order to determine individual layer thicknesses of the multilayer stack taking into account the measured nitrogen content of the nitrided films. The procedure adhered to the prescriptions of ISO18118:2004(E) for the calculations of inelastic mean free paths (IMFP) and elastic corrections thereof, using film material properties, like densities and band gaps. Effective attenuation lengths (EAL) were taken throughout as 90% of the respective IMFP, whereas an appropriate set of empirical relative sensitivity factors (RSF) was used. The XPS‐derived thicknesses were compared with corresponding values obtained from medium‐energy ion scattering (MEIS) measurements on the same series of specimens in combination with energy spectrum simulation to provide quantitative layer information with sub‐nanometer resolution. The XPS and MEIS results exhibit very good agreement on the deduced layer structures within the respective experimental uncertainty, and both sets are consistent with the grown nominal layer parameters of the high‐k nanofilms. Copyright © 2010 John Wiley &amp; Sons, Ltd.
The effect of overlap-masking on binaural reverberant word intelligibility (2004)

Reverberation interferes with the ability to understand speech in rooms. Overlap-masking explains this degradation by assuming reverberant phonemes endure in time and mask subsequent reverberant phonemes. Most listeners benefit from binaural listening when reverberation exists, indicating that the listener's binaural system processes the two channels to reduce the reverberation. This paper investigates the hypothesis that the binaural word intelligibility advantage found in reverberation is a result of binaural overlap-masking release with the reverberation acting as masking noise. The tests utilize phonetically balanced word lists (ANSI-S3.2 1989), that are presented diotically and binaurally with recorded reverberation and reverberation-like noise. A small room, 62 m3, reverberates the words. These are recorded using two microphones without additional noise sources. The reverberation-like noise is a modified form of these recordings and has a similar spectral content. It does not contain binaural localization cues due to a phase randomization procedure. Listening to the reverberant words binaurally improves the intelligibility by 6.0% over diotic listening. The binaural intelligibility advantage for reverberation-like noise is only 2.6%. This indicates that binaural overlap-masking release is insufficient to explain the entire binaural word intelligibility advantage in reverberation.
ChemInform Abstract: Cycloadditions of 1,3‐Oxazolium‐4‐olates (Isomuenchnones) by Rhodium( II)‐Induced Decomposition of α‐Diazocarbonyl Derivatives of (5R)‐ and (5S)‐Phenyloxazin‐3‐one as a Chiral Template. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Minimum complexity decoupling networks for arbitrary coupled loads (2014)

Decoupling networks that match N coupled loads to N decoupled sources can be realized by generalized Π-networks of reactive impedances. For a set of N coupled loads, the realization of the decoupling network is not unique, and networks that involve many impedances can be difficult to lay out on circuit boards. In this paper, we establish that a decoupling network requires a minimum of N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + N impedances for N arbitrarily coupled loads, and provide examples constructed by a systematic method that realizes this lower bound.