gebhart/patrepeval huggingface dataset:
Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites (2016)

The Arabidopsis carotenoid cleavage dioxygenase 4 (AtCCD4) is a negative regulator of the carotenoid content of seeds and has recently been suggested as a candidate for the generation of retrograde signals that are thought to derive from the cleavage of poly-cis-configured carotene desaturation intermediates. In this work, we investigated the activity of AtCCD4 in vitro and used dynamic modeling to determine its substrate preference. Our results document strict regional specificity for cleavage at the C9-C10 double bond in carotenoids and apocarotenoids, with preference for carotenoid substrates and an obstructing effect on hydroxyl functions, and demonstrate the specificity for all-trans-configured carotenes and xanthophylls. AtCCD4 cleaved substrates with at least one ionone ring and did not convert acyclic carotene desaturation intermediates, independent of their isomeric states. These results do not support a direct involvement of AtCCD4 in generating the supposed regulatory metabolites. In contrast, the strigolactone biosynthetic enzyme AtCCD7 converted 9-cis-configured acyclic carotenes, such as 9-cis-ζ-carotene, 9'-cis-neurosporene, and 9-cis-lycopene, yielding 9-cis-configured products and indicating that AtCCD7, rather than AtCCD4, is the candidate for forming acyclic retrograde signals.
Screening the ToxCast Phase 1, Phase 2, and e1k Chemical Libraries for Inhibitors of Iodothyronine Deiodinases (2018)

Deiodinase enzymes play an essential role in converting thyroid hormones between active and inactive forms by deiodinating the pro-hormone thyroxine (T4) to the active hormone triiodothyronine (T3) and modifying T4 and T3 to inactive forms. Chemical inhibition of deiodinase activity has been identified as an important endpoint to include in screening chemicals for thyroid hormone disruption. To address the lack of data regarding chemicals that inhibit the deiodinase enzymes, we developed robust in vitro assays that utilized human deiodinase types 1, 2, and 3 and screened over 1800 unique chemicals from the U.S. EPA's ToxCast phase 1_v2, phase 2, and e1k libraries. Initial testing at a single concentration identified 411 putative deiodinase inhibitors that produced inhibition of 20% or greater in at least 1 of the 3 deiodinase assays, including chemicals that have not previously been shown to inhibit deiodinases. Of these, 228 chemicals produced enzyme inhibition of 50% or greater; these chemicals were further tested in concentration-response to determine relative potency. Comparisons across these deiodinase assays identified 81 chemicals that produced selective inhibition, with 50% inhibition or greater of only 1 of the deiodinases. This set of 3 deiodinase inhibition assays provides a significant contribution toward expanding the limited number of in vitro assays used to identify chemicals with the potential to interfere with thyroid hormone homeostasis. In addition, these results set the groundwork for development and evaluation of structure-activity relationships for deiodinase inhibition, and inform targeted selection of chemicals for further testing to identify adverse outcomes of deiodinase inhibition.
An 80W Power Amplifier with 50% Efficiency at 8dB Power Back-off over 2.6-3.8 GHz (2019)

This paper presents the design and implementation of a wideband power amplifier (PA) suitable for applications using signals with large peak-to-average-power-ratio (PAPR). The proposed design approach is based on reducing the load modulation factor compared to conventional Doherty PA. To demonstrate the principle, a PA that operates between 2.55 GHz and 3.8 GHz has been implemented and tested. In this frequency range, the measured peak output power is 49.3 ± 0.5 dBm and the measured drain efficiency is between 47-60 % for output power levels corresponding to 8 dB output back-off (OBO).
Non-alcoholic fatty liver disease: need for a balanced nutritional source (2014)

Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) are an increasingly common chronic liver disease closely associated with diabetes and obesity that have reached epidemic proportions. Reports on the prevalence of NAFLD have suggested that 27-34% of the general population in the USA and 40-90% of the obese population worldwide have this disease. Increasing urbanisation rate and associated inappropriate lifestyle changes are not only the risk factors of diabetes, but also unmask genetic predisposition in various populations for the metabolic syndrome and its manifestations including NAFLD and NASH. Lifestyle modifications and balanced nutrition are among the foremost management strategies along with ursodeoxycholic acid, metformin, vitamin E and pentoxifylline. Although weight reduction associated with current therapeutic strategies has shown some promise, maintaining it in the long run is largely unsuccessful. With the safety of pharmacotherapy still being uncertain and can be started only after confirmation, other reasonable interventions such as nutrition hold promise in preventing disease progression. The role of dietary components including branched-chain amino acids, methionine, choline and folic acid is currently being evaluated in various clinical trials. Nutritional approaches sought to overcome the limitations of pharmacotherapy also include evaluating the effects of natural ingredients, such as silymarin and spirulina, on liver disease. Understanding the specific interaction between nutrients and dietary needs in NAFLD and maintaining this balance through either a diet or a nutritional product thus becomes extremely important in providing a more realistic and feasible alternative to treat NAFLD. A planned complete nutritional combination addressing specific needs and helping to prevent the progression of NAFLD is the need of the hour to avert people from ending up with complications.
&lt;title&gt;ESPI-FEM hybrid system for studies of time-dependent stress characteristics in small components&lt;/title&gt; (1995)

Understanding and quantitative modeling of stress relaxation processes are very important for reliable and efficient design of the load resisting structures. In this paper a hybrid ESPI-FEM system for evaluation of time-dependent stress and strain characteristics in small components is presented. Based on results obtained by this method a long term prediction of material behavior can be done. Problems related to the coupling of results from the experiment to an FEM model are discussed and illustrated with reference to speckle interferometry stress analysis of a cantilever beam. Results show that for the conditions tested, stress level in the cantilever beam reduces by 10% of the level at the instant of the loading.
Low Velocity Impact Strength of CFRP Composites Incorporating Nanoclay (2015)

Carbon fiber reinforced polymer (CFRP) composites are the most commonly used material for aerospace applications. Damage of CFRP composites due to low-velocity impact from hail or small cosmic particles on airplanes or aerospace structures have been reported as a critical issue in aerospace applications. Since CFRP off-axis and out-of-plane responses strongly depend on matrix properties, we hypothesize that altering the matrix properties of CFRP using nanomaterials might result in a significant improvement in the low-velocity impact strength of CFRP. In this work, we present the use of nanoclay as a natural material with good chemical modification responses and a relatively low cost. Two loadings of nanoclay by weight of epoxy resin were examined; 4.0 wt.% and 10.0 wt.%. CFRP composite plates were produced using the epoxy-clay nanocomposites. The CFRP plates were then subjected to impact energy of 9 and 18 J representing a typical range for lowvelocity impact. Time-history response of load, displacement and velocity were monitored and reported. Moreover, 3D computer models generated from x-ray computed tomography (CT) scans of the impacted CFRP were examined to quantify the level of damage in CFRP. Finally, microstructural characterization was also performed to understand the significance of nanoclay intercalation on the behavior of CFRP composites fabricated using the modified nanocomposite. It was concluded that low content of nanoclay (4.0 wt.%), representing exfoliated platelets, does not have a significant effect on the low-velocity impact strength of CFRP. However, a relatively high content of nanoclay (10.0 wt.%), representing intercalated nanoclay platelets, has a significant improvement of the low velocity impact strength of CFRP. However, it was observed that these enhancements at 10.0 wt.% are associated with embrittlement of CFRP composite under impact. It is demonstrated that quantifying low velocity impact damage in CFRP using CT-scans might be possible for relatively low damage levels.
Supplementary Table 2 from Circulating B-Cell Chronic Lymphocytic Leukemia Cells Display Impaired Migration to Lymph Nodes and Bone Marrow (2023)

Supplementary Table 2 from Circulating B-Cell Chronic Lymphocytic Leukemia Cells Display Impaired Migration to Lymph Nodes and Bone Marrow
Abstract 15976: Results of the Full Cox-Maze Procedure: EKG vs 24-Hour Holter vs One-Week Long-Term Holter Monitoring (2014)

Introduction: Much of work published on Cox-Maze procedure results has utilized EKGs or 24-hour Holter without information on anti-arrhythmic drugs (AAD). The purpose of this study was to explore results at 6 and 24 months following the Cox-Maze procedure using various rhythm monitoring techniques. Hypothesis: It was hypothesized that long-term monitoring (LTM) would identify more patients who experienced atrial arrhythmia (AA) at each time point than other monitoring techniques. Methods: Cox-Maze III/IV patients off AAD were offered 1-week LTM with n=220 at 6 and n=94 at 24 months. EKG, 24-hour Holter, and LTM were ascertained at the same time. The HRS definition (AA &gt;30 seconds) was used for ablation failure. Results: At 6 months EKG found n=216 returned to sinus rhythm (SR), 24-hr Holter found n=211 returned to SR, while n=203 were in SR by LTM (FIGURE). Of patients experiencing AA at 6 months, duration &lt;1 hour was documented in 56% by 24-hr Holter and 59% by LTM (FIGURE). At 24 months, EKG found n=89 returned to SR, 24-hr Holter found n=88 returned to SR, while n=85 were in SR by LTM. Of patients experiencing AA at 24 months, duration &lt;1 hour was documented in 50% by 24-hr Holter and 67% by LTM. At 6 months, percent in SR differed for EKG vs LTM (p&lt;0.001) and 24-hr Holter vs LTM (p=0.02). At 24 months, monitoring methods did not differ. Conclusions: The Cox-Maze procedure demonstrated high return to SR off AAD, regardless of monitoring technique. However, LTM provides more accuracy earlier in postoperative period and should be used when discussing discontinuation of anticoagulation. Due to clinical and financial challenges in applying LTM, patients in which LTM has most value should be identified.
Prediction of Lost Circulation Zones Using Artificial Neural Network and Functional Network (2020)

Abstract Drilling high-pressure high-temperature (HPHT) wells lead to many difficulties and issues. One of the most difficulties during the drilling is the loss of circulation. 40% of the drilling's cost is belong to the drilling fluid, so the loss of these fluid causes an increasing in the total drilling operation's cost. Circulation loss has many consequences related to well control which can lead to the worst case of blowout. There are several approaches to avoid loss of return, one of these approaches is preventing the occurrence of the losses by identifying the lost circulations zones. However, most of these approaches are difficult to be applied due to some constraints in the field. The purpose of this work is to apply two artificial intelligence (AI) techniques to identify the zones of lost circulation. A data of real-time surface drilling parameters from three wells were obtained using real-time drilling sensors. The two methods of AI are functional networks (FN) and artificial neural networks (ANN). Well (A) was utilized to build the two AI models by dividing their data into training and testing. Then, well (B) was utilized to validate the developed AI models. A high accuracy was achieved by the two AI models based on the root mean squared error (RMSE), confusion matrix and correlation coefficient (R). Both AI models identified the zones of lost circulation in Well A with high accuracy where the R is more than 0.98 and RMSE is less than 0.09. ANN is the most accurate model with R = 0.99 and RMSE = 0.05. Moreover, ANN was able to predict the lost circulation zones in the unseen well B (R = 0.952 and RMSE = 0.155).
Performance of 5-Strand Hamstring Autograft Anterior Cruciate Ligament Reconstruction in the STABILITY Study: A Subgroup Analysis (2022)

At the 24-month follow-up, there were no significant differences in clinical failure rates and PROs in an analysis of patients with 4S and 5S hamstring autografts of ≥8mm diameter for ACLR or ACLR + LET. The 5S hamstring graft configuration is a viable option to produce larger-diameter ACL grafts.
Gene Expression and the Physiological Role of Transforming Growth Factor-α in the Mouse Pituitary (2003)

Transforming growth factor-alpha (TGF-alpha), a member of the epidermal growth factor (EGF) family, is produced within the mouse anterior pituitaries. However, the cell types of TGF-alpha-expressing cells and the physiological roles of TGF-alpha within mouse pituitary glands remain unclear. The aim of the present study was to localize TGF-alpha mRNA-expressing cells, and to clarify the involvement of TGF-alpha in estrogen-induced DNA replication in mouse anterior pituitary cells. Northern blot analysis demonstrated TGF-alpha mRNA expression in adult male and female mouse anterior pituitaries. In situ hybridization analysis of the pituitaries in these mice showed that TGF-alpha mRNA-expressing cells in the anterior pituitary are round, oval, and medium-sized. TGF-alpha mRNA was colocalized in most of the growth hormone (GH) mRNA-expressing cells, while only some of the prolactin (PRL) mRNA-expressing cells. DNA replication in the anterior pituitary cells was detected by monitoring the cellular uptake of a thymidine analogue, bromodeoxyuridine (BrdU) in a primary serum-free culture system. Estradiol-17beta (E2) and TGF-alpha treatment increased the number of BrdU-labelled mammotrophs, indicating that E2 and TGF-alpha treatment stimulates the DNA replication in mammotrophs. Immunoneutralization of TGF-alpha with anti-TGF-alpha-antibodies nullified the E2-induced increase in DNA replication. RT-PCR analysis of TGF-alpha mRNA expression in ovariectomized female mice revealed that E2 increases TGF-alpha mRNA levels. These results indicate that the TGF-alpha produced primarily in the somatotrophs mediates the stimulatory effects of estrogen on the DNA replication of pituitary cells in a paracrine or autocrine manner.
Chemistry of Potent Anti-Cancer Compounds, Amphidinolides (2001)

Amphidinolides A-V represent a family of cytotoxic marine natural products with diverse structural features and pronounced biological activities. Kobayashi and his research group have been reporting over the years the discoveries of these remarkable molecules, one after another, since 1986 when the first report of the series appeared. Thanks to their perseverance and painstaking research, the family is still expanding. The unique structural features and biological activity profiles of these macrolides have obviously attracted the attention of organic chemists worldwide. The total syntheses of three members of the family, amphidinolides J, K and P, have already been achieved. This review tries to chronicle the fascinating chemistries of amphidinolides, studies on the syntheses of some of these molecules and their biological activity profiles.
<i>Ad hoc</i> solid electrolyte on acidized carbon nanotube paper improves cycle life of lithium–sulfur batteries (2017)

The <italic>in situ</italic> polymerized solid barrier stops sulfur transport while still allowing bidirectional Li<sup>+</sup> transport, alleviating the shuttle effect and increasing the cycling performance.
A Review of Cyber–Physical Security for Photovoltaic Systems (2021)

In this article, the challenges and a future vision of the cyber–physical security of photovoltaic (PV) systems are discussed from a firmware, network, PV converter controls, and grid security perspective. The vulnerabilities of PV systems are investigated under a variety of cyberattacks, ranging from data integrity attacks to software-based attacks. A success rate metric is designed to evaluate the impact and facilitate decision-making. Model-based and data-driven methods for threat detection and mitigation are summarized. In addition, the blockchain technology that addresses cyberattacks in software and cybernetworks is described. Simulation and experimental results that show the impact of cyberattacks at the converter (device) and grid (system) levels are presented. Finally, potential research opportunities are discussed for next-generation, cybersecure power electronics systems. These opportunities include multiscale controllability, self-/event-triggering control, artificial intelligence/machine learning, hot patching, and online security. As of today, this study will be one of the few comprehensive studies in this emerging and fast-growing area.
RNA Interference Therapy for Chronic Hepatitis B Predicts the Importance of Addressing Viral Integration When Developing Novel Cure Strategies (2021)

Chronic hepatitis B infection remains a globally important cause of morbidity and mortality and has recently undergone a renaissance in therapeutic interest with increased pre-clinical and clinical testing of new drug classes. One of the first new classes in the clinic was RNA interference agents, which have the potential to impact the entire viral life cycle by reducing all virus-produced mRNA. Early clinical testing with the first of these agents in the clinic, ARC-520, demonstrated that rapid and deep reductions in viral proteins, RNA and DNA could be produced with this approach, but also the surprising insight that HBsAg production from incomplete HBV DNA integrated into the host genome appears to play a heretofore unappreciated and important role in maintaining circulating HBsAg, thought to play a fundamental role in preventing host clearance of the virus. Thus, accounting for viral DNA integration in novel HBV treatment approaches may prove to be essential to achieving successful finite therapies of this difficult to treat chronic infection.
Single Molecule Analysis of CENP-A Chromatin by High-Speed Atomic Force Microscopy (2022)

Abstract Chromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated in the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamics in vitro inform us about chromatin accessibility in vivo . By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the MSD and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo . Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. Thus, changes which alter chromatin accessibility in vitro , also correspondingly alter transcription in vivo . These data suggest a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance mobility.
Abstract 11241: Longitudinal Myocardial Mechanics in Covid-19 Survivors with Normal Left Ventricular Ejection Fraction, a Single Center Study (2021)

Introduction: Subclinical cardiovascular involvement in COVID-19 patients has not been well described. 2D-Speckle Tracking Echocardiography derived global longitudinal strain (GLS) and systolic and early diastolic strain rate (SRs, SRe) measurements are more sensitive than standard echocardiographic parameters to diagnose subclinical mechanical dysfunction in patients with normal Left Ventricle Ejection Fraction (LVEF). Hypothesis: Evaluate subclinical myocardial mechanical function and reserve in active COVID-19 systemic disease patients with normal LVEF vs controls and between survivors and non survivors of COVID-19 in the longitudinal domain of contractility. Methods &amp; Results: 166 adult patients with active COVID 19 having normal LVEF were included and compared to 89 healthy volunteers. Baseline parameters were recorded. Peak GLS, SRs and SRe, were measured offline. Mean age was 62.53 ± 18.96 years and 87 (52%) were males and Mean LVEF was 62±5%. COVID-19 patients had higher GLS compared to controls (-20.93%±0.30 vs. -18.48%±0.40; p value &lt;0.0001), SRs was similar (-0.97 s -1 ±0.10 vs. -0.98 s -1 ±0.02, p value 0.2528) and SRe was lower (0.85 s -1 ±0.0 vs. 1.05 s -1 ±0.02; p value &lt;0.0001) respectively. After adjusting for age and sex, GLS, SRs and SRe was significant (p&lt;0.001). GLS, SRs and SRe were similar in survivors vs. non survivors (p NS), both groups had elevated biomarkers (cardiac troponin, NT-pro BNP, CRP), but non survivors had higher levels (3.22±0.18 vs 3.62±0.28, p = 0.2371, 5.86±0.19 vs 7.15±0.27, p = 0.0004, 3.75±0.14 vs 4.31±0.21, p = 0.0422, 7.64±0.17 vs 8.26±0.25, p=0.0487 respectively) (Table 1). Conclusions: In our cohort, COVID-19 patients had better systolic reserve and abnormal relaxation compared to controls. There was no significant difference in strain (GLS) and strain rate (SRs &amp; SRe) amongst survivors and non survivors in the longitudinal domain of contractility despite of higher inflammatory biomarkers in non-survivors.
Neurally adjusted ventilatory assist and proportional assist ventilation both improve patient-ventilator interaction (2015)

Clinicaltrials.gov NCT02056093 . Registered 18 December 2013.
Advances in neuroimaging of traumatic brain injury and posttraumatic stress disorder (2009)

Improved diagnosis and treatment of traumatic brain injury (TBI) and posttraumatic stress disorder (PTSD) are needed for our military and veterans, their families, and society at large. Advances in brain imaging offer important biomarkers of structural, functional, and metabolic information concerning the brain. This article reviews the application of various imaging techniques to the clinical problems of TBI and PTSD. For TBI, we focus on findings and advances in neuroimaging that hold promise for better detection, characterization, and monitoring of objective brain changes in symptomatic patients with combat-related, closed-head brain injuries not readily apparent by standard computed tomography or conventional magnetic resonance imaging techniques.