gebhart/patrepeval huggingface dataset:
Supplementary Figure 2 from A Genome-Scale RNA Interference Screen Implicates NF1 Loss in Resistance to RAF Inhibition (2023)

&lt;p&gt;Supplementary Figure 2 PDF file - 45K, Resistance to the MEK inhibitor AZD6244 induced by loss of NF1 is reversed by combined suppression of C-RAF by RNA interference. A375 cells were infected with the indicated shRNAs and then exposed to a 10-point titration of the MEK inhibitor AZD6244 for 4 d. Cell proliferation was assessed using cell-titer glo&lt;/p&gt;
Supplementary Figures S1 - S6, Tables S1 - S2 from Multigene Profiling of CTCs in mCRPC Identifies a Clinically Relevant Prognostic Signature (2023)

&lt;p&gt;Supplementary Figure S1: Evaluation of pre-amplication. Supplementary Figure S2: Algorithm for CTC positivity. Supplementary Figure S3: CTC isolation and gene analysis methodology. Supplementary Figure S4: Validation of gene expression. Supplementary Figure S5: CTC status is not predictive of overall survival. Supplementary Figure S6: miCTC score flowsheet. Supplementary Table 1: primer tables. Supplementary Table 2: Ct values.&lt;/p&gt;
Promotion of methane storage capacity with metal–organic frameworks of high porosity (2022)

The effect of storage conditions on the optimal MOF pore volume and methane working capacity has been analyzed, and the benchmark NPF-200 was discovered.
Self-adhesive resin cements - chemistry, properties and clinical considerations (2010)

Self-adhesive resin cements were introduced to dentistry within the past decade but have gained rapidly in popularity with more than a dozen commercial brands now available. This review article explores their chemical composition and its effect on the setting reaction and adhesion to various substrates, their physical and biological properties that may help to predict their ultimate performance and their clinical performance to date and handling characteristics. The result of this review of self-adhesive resin cements would suggest that these materials may be expected to show similar clinical performance as other resin-based and non-resin based dental cements.
Supplementary Table 1 from <i>JAK3</i> Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients (2023)

&lt;p&gt;Differences in the frequency of somatic mutations observed in Non-Latino Whites and Black HNSCC patients.&lt;/p&gt;
Tracking Charge Transfer to Residual Metal Clusters in Conjugated Polymers for Photocatalytic Hydrogen Evolution (2020)

Semiconducting polymers are versatile materials for solar energy conversion and have gained popularity as photocatalysts for sunlight-driven hydrogen production. Organic polymers often contain residual metal impurities such as palladium (Pd) clusters that are formed during the polymerization reaction, and there is increasing evidence for a catalytic role of such metal clusters in polymer photocatalysts. Using transient and operando optical spectroscopy on nanoparticles of F8BT, P3HT, and the dibenzo[<i>b,d</i>]thiophene sulfone homopolymer P10, we demonstrate how differences in the time scale of electron transfer to Pd clusters translate into hydrogen evolution activity optima at different residual Pd concentrations. For F8BT nanoparticles with common Pd concentrations of >1000 ppm (>0.1 wt %), we find that residual Pd clusters quench photogenerated excitons via energy and electron transfer on the femto-nanosecond time scale, thus outcompeting reductive quenching. We spectroscopically identify reduced Pd clusters in our F8BT nanoparticles from the microsecond time scale onward and show that the predominant location of long-lived electrons gradually shifts to the F8BT polymer when the Pd content is lowered. While a low yield of long-lived electrons limits the hydrogen evolution activity of F8BT, P10 exhibits a substantially higher hydrogen evolution activity, which we demonstrate results from higher yields of long-lived electrons due to more efficient reductive quenching. Surprisingly, and despite the higher performance of P10, long-lived electrons reside on the P10 polymer rather than on the Pd clusters in P10 particles, even at very high Pd concentrations of 27000 ppm (2.7 wt %). In contrast, long-lived electrons in F8BT already reside on Pd clusters before the typical time scale of hydrogen evolution. This comparison shows that P10 exhibits efficient reductive quenching but slow electron transfer to residual Pd clusters, whereas the opposite is the case for F8BT. These findings suggest that the development of even more efficient polymer photocatalysts must target materials that combine both rapid reductive quenching and rapid charge transfer to a metal-based cocatalyst.
The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response (2022)

SUMMARY Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms triggered by the infected cell. The successful completion of the replicative viral cycle within a cell depends on the function of viral components versus the cellular defenses. Non-coding RNAs (ncRNAs) are important cellular modulators, either promoting or preventing the progression of viral infections. Among these ncRNAs, the long non-coding RNA (lncRNA) family is especially relevant due to their intrinsic functional properties and ubiquitous biological roles. Specific lncRNAs have been recently characterized as modulators of the cellular response during infection of human host cells by single stranded RNA viruses. However, the role of host lncRNAs in the infection by human RNA coronaviruses such as SARS-CoV-2 remains uncharacterized. In the present work, we have performed a transcriptomic study of a cohort of patients with different SARS-CoV-2 viral load. Our results revealed the existence of a SARS-CoV-2 infection-dependent pattern of transcriptional up-regulation in which specific lncRNAs are an integral component. To determine the role of these lncRNAs, we performed a functional correlation analysis complemented with the study of the validated interactions between lncRNAs and RNA-binding proteins (RBPs). This combination of in silico functional association studies and experimental evidence allowed us to identify a lncRNA signature composed of six elements - NRIR, BISPR, MIR155HG, FMR1-IT1, USP30-AS1, and U62317.2 - associated with the regulation of SARS-CoV-2 infection. We propose a competition mechanism between the viral RNA genome and the regulatory lncRNAs in the sequestering of specific RBPs that modulates the interferon response and the regulation of RNA surveillance by nonsense-mediated decay (NMD). Abstract Figure Graphical abstract Model of interactions among lncRNA and cognate RNA-binding proteins in SARS-CoV-2 infection. According to our model, the viral genome can establish direct interactions with three core proteins (DDX3X, UPF1 and IGF2BP2) involved in mRNA metabolism and regulation of the interferon response, which are also components of a SARS-CoV-2 lncRNA-centered regulatory network. The competition between viral RNA and lncRNAs could act as a counteracting factor for the normal function of homeostatic lncRNA-centered regulatory networks, contributing to viral progression and replication. Black arrows depict physical interactions between network components; red arrows represent functional relationships.
Activin A more prominently regulates muscle mass in primates than does GDF8 (2017)

Growth and differentiation factor 8 (GDF8) is a TGF-β superfamily member, and negative regulator of skeletal muscle mass. GDF8 inhibition results in prominent muscle growth in mice, but less impressive hypertrophy in primates, including man. Broad TGF-β inhibition suggests another family member negatively regulates muscle mass, and its blockade enhances muscle growth seen with GDF8-specific inhibition. Here we show that activin A is the long-sought second negative muscle regulator. Activin A specific inhibition, on top of GDF8 inhibition, leads to pronounced muscle hypertrophy and force production in mice and monkeys. Inhibition of these two ligands mimics the hypertrophy seen with broad TGF-β blockers, while avoiding the adverse effects due to inhibition of multiple family members. Altogether, we identify activin A as a second negative regulator of muscle mass, and suggest that inhibition of both ligands provides a preferred therapeutic approach, which maximizes the benefit:risk ratio for muscle diseases in man.
Single Step Solution Processed GaAs Thin Films from GaMe3 and tBuAsH2 under Ambient Pressure (2016)

This article reports on the possibility of low-cost GaAs formed under ambient pressure via a single step solution processed route from only readily available precursors, tBuAsH2 and GaMe3. The thin films of GaAs on glass substrates were found to have good crystallinity with crystallites as large as 150 nm and low contamination with experimental results matching well with theoretical density of states calculations. These results open up a route to efficient and cost-effective scale up of GaAs thin films with high material properties for widespread industrial use. Confirmation of film quality was determined using XRD, Raman, EDX mapping, SEM, HRTEM, XPS, and SIMS.
Integration of the metabolic and cardiovascular effects of exercise (2006)

Most of the essays in this volume have adopted a reductionist approach and have focused on the biochemistry either in skeletal muscle or in the vascular wall. There is however a complex interaction between the biochemistry in the endothelium of the microvascular wall, the vascular smooth muscle and the skeletal muscle fibres involving signalling pathways in the three tissues and an intense exchange of signal molecules between them. In the present essay an integrative overview is given of this complex metabolic interaction and the impairments in it that lead to type 2 diabetes and cardiovascular disease.A reduced nitric oxide production by the (micro)vascular endothelium is identified as the key event and is reversible by regular exercise and a reduced calorie intake. The chapter also contains a description of the complex metabolic network controlled by the inducible transcription factor nuclear factor-kappaB, that is activated in more advanced stages of the chronic diseases, and either leads to repair of the microvascular wall or to irreversible damage and the severe complications of end stage cardiovascular disease and type 2 diabetes.
Low-power current-mode transceiver for on-chip bidirectional buses (2010)

This paper presents a current-mode signalling scheme for bidirectional long on-chip interconnects. The transceiver has been fabricated in 180nm CMOS process. Features of the proposed scheme are driver pre-emphasis and low impedance termination. While no extra repeater is needed for line lengths up to 8mm long the scheme improves the delay by 34% for 2mm-8mm long lines, compared to bidirectional voltage-mode links. The scheme also improves the power performance for line lengths longer than 2mm, operating at data rates higher than 180Mbps. Measurement results show that delay and power-delay product improve by 18% and 3.7x, respectively, compared to simulation results of the voltage-mode scheme.
Effectiveness of Radial-Gain Tailoring in Large-Mode-Area Fiber Lasers and Amplifiers (2007)

Analytic expressions are derived for modal discrimination in large-mode-area gain-tailored fibers. While Gaussian-like profiles result in increased modal discrimination, step-gain profiles smaller than the waveguide core offer the highest discrimination.
Crystal Structures and Local Environments of NASICON-Type Na3FeV(PO4)3 and Na4FeV(PO4)3 Positive Electrode Materials for Na-Ion Batteries (2021)

In this work, we investigate the crystal chemistry of Fe/V-mixed NASICON [sodium (Na) Super Ionic CONductor] compositions Na3FeV(PO4)3 and Na4FeV(PO4)3 that are structurally related to Na3V2(PO4)3, a positive electrode for Na-ion batteries. To synthesize Na4FeV(PO4)3, various synthesis routes (solid-state, sol–gel-assisted, and electrochemical syntheses) were investigated. Direct syntheses resulted in the formation of a NASICON-type phase in the presence of NaFePO4 and Na3PO4 impurities. The successful preparation of pure Na4FeV(PO4)3 has been achieved by the electrochemical sodiation of Na3FeV(PO4)3. Both synchrotron X-ray absorption and Mössbauer spectroscopy allowed probing the local V and Fe environments and their oxidation states in Na3FeV(PO4)3 and Na4FeV(PO4)3. Na3FeV(PO4)3 crystallizes in the space group C2/c (a = 15.1394(2) Å; b = 8.72550(12) Å; c = 21.6142(3) Å; β = 90.1744(9)°; and Z = 12), and it is isostructural to an ordered α-form of Na3M2(PO4)3 (M = Fe, V). It presents a superstructure due to Na+ ordering, as confirmed by differential scanning calorimetry and in situ temperature X-ray diffraction. The electrochemically sodiated Na4FeV(PO4)3 powder crystallizes in the space group R3̅c (a = 8.94656(8) Å, c = 21.3054(3) Å, and Z = 6) within which the two sodium sites, Na(1) and Na(2), are almost fully occupied. Na4FeV(PO4)3 allows the electrochemical extraction of 2.76 Na+ per formula unit within the voltage range of 1.3–4.3 V versus Na+/Na through the FeIII/II, VIV/III, and VV/IV redox couples. This identifies an interesting material for Na-ion batteries.
Gene Therapy Approaches for Treating Rheumatoid Arthritis (2000)

Current gene therapy approaches for treating rheumatoid arthritis have made use of gene transfer technology as an improved delivery system for emerging proteins and other biologicals whose activities may have therapeutic value. Preclinical research has focused on two primary directions, evaluation of methods of gene delivery and identification of gene products with antiarthritic potential. Although there are reports involving systemic gene delivery, the bulk of effort has focused on local, intraarticular administration using ex vivo and in vivo methods. Viral-based vectors, including adenovirus, adeno-associated virus and herpes simplex virus have the greatest efficiency of gene delivery after intraarticular injection and are capable of generating relevant levels of gene products in several animal models of disease. However, there are limitations to existing generations of these systems that currently preclude their clinical application. Those gene products found to be efficacious in animal models of rheumatoid arthritis include proteins that specifically block the activity of the primary inflammatory cytokines, and include interleukin-1 receptor antagonist and soluble receptors for tumor necrosis factor and interleukin-1. Delivery and expression of genes encoding certain cytokines such as interleukins -4, -10, and -13 and viral interleukin-10, that block synthesis of inflammatory mediators and downregulate aspects of cellular and humoral immune pathways have been found beneficial. Although significant progress has been made, leading to Phase I clinical trials, there remain several hurdles to the routine practice of gene therapy for treatment of rheumatoid arthritis.
Pulmonary Hypertension in Patients Undergoing Transcatheter Aortic Valve Replacement (2015)

1P ulmonary hypertension (PH) is a significant, often irrevers- ible, risk factor of early and late morbidity and mortality in patients undergoing transcatheter aortic valve replacement (TAVR).The widely used Society of Thoracic Surgeons (STSs) Predicted Risk of Mortality (STS-Predicted Risk of Mortality) risk score does not include PH and the commonly associated right ventricular (RV) dysfunction.Therefore, procedural risk of patients with severe PH undergoing TAVR is probably underestimated and consideration of its risk relies heavily on clinical, procedural, and anecdotal experience.In addition, literature on the management of patients with severe PH undergoing TAVR is scarce.Using 1 of our recent transapical TAVR patients as an illustrative example we, therefore, sought to discuss recent data on outcomes of patients with severe PH undergoing TAVR, emerging TAVR risk scores that incorporate severe PH and other TAVR-specific risk factors as well as a guideline on how to clinically manage patients with severe PH undergoing TAVR who often present as difficult hemodynamic challenges. Case PresentationAn 82-year-old (body mass index, 26.8 kg/m 2 ) insulin-dependent diabetic female (151 cm, 62 kg) with symptomatic severe calcific aortic stenosis (echocardiographically derived: mean transvalvular gradient 43 mm Hg, maximal velocity 4.3 m/s and a calculated valve area of 0.5 cm 2 ) and preserved left ventricular (LV) function with an ejection fraction of 60%.She has severe coronary artery disease, is status post coronary artery bypass graft surgery with patent grafts to left anterior descending and ramus intermedius; the circumflex artery is only moderately diseased and the right coronary artery is small, nondominant with mild, diffuse disease (<1.5 mm in size).The right heart hemodynamics are summarized in Figure 1 and Table 1 with mild-to-moderate right heart failure (increased RV end-diastolic pressure) and severe mixed PH with a low-normal cardiac output.Her pulmonary artery wedge pressure (PAWP) was high without a dominant v wave.Because her echocardiogram did not show significant mitral valve nor aortic valve regurgitation, the high filling pressures were felt secondary to the long standing severe aortic valve stenosis with LV hypertrophy and associated LV diastolic dysfunction.The echocardiogram showed furthermore a preserved RV function with mild RV enlargement.We did not assess her pulmonary vascular reactivity during the right heart catheterization.She had no history of pulmonary thromboembolism or pulmonary disease, her preoperative pulmonary function test was within normal limits.Her most recent laboratory data are summarized in Table 2.Because of her cardiovascular history, comorbidities, and high STS risk score (10.8%), our heart team decided to offer TAVR.Because of significant peripheral vascular disease (<6-mm-sized iliac arteries bilaterally), she underwent transapical TAVR with a 23-mm Edwards Sapien valve.
A new stapler-based full-thickness transgastric access closure: results from an animal pilot trial (2007)

Gastrotomy closure with a perorally delivered flexible stapling device created a leak-resistant transmural line of staples followed by full-thickness healing of the gastric wall incision. Increasing the length of the instrument and adding device articulation will further facilitate its use for NOTES procedures.
Underwater channel estimation and tracking using mixed norm optimization techniques. (2009)

A mixed norm optimization technique to track the impulse response of the underwater acoustic channel is presented. The channel is assumed to follow a delay-Doppler spread function model, which is known to be sparsely distributed over the complex channel coefficients. The ill-conditioned nature of this estimation problem, along with the need to optimize over a complex field, poses challenges to employing popular sparse estimation techniques that currently exist in the literature. The time-varying nature of the underwater channel also makes efficient tracking difficult. The motivation behind our proposed algorithm is to robustly estimate and efficiently track the sparse delay-Doppler coefficients directly over the complex field. We have formulated the channel estimation problem as that of minimizing over a convex combination of the L1 norm of the sparse coefficients to be estimated and the L2 norm of the estimation error. We analyze the difference between our proposed algorithm to existing L2-constrained L1 optimization techniques and present results showing performance on simulation generated and field data. [Work supported in part by ONR Grant Nos. N00014-05-10085 and N00014-07-10184 and in part by Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Doherty Foundation.]
Factors affecting in vitro gastric mucoadhesion. III. Influence of polymer addition on the observed mucoadhesion of some materials (1996)

It has previously been demonstrated that experimental conditions and the physical properties of polymers can significantly influence the observed results for in vitro gastric mucoadhesion. This work summarizes the influence of added polymers on the observed mucoadhesion of materials previously shown to have strong mucoadhesive properties in the test system. It is demonstrated that the inclusion of 5% of a grade of polyvinylpyrrolidone, PVP K30, can significantly reduce the adhesion of all the mucoadhesive materials tested. These included a range of polyacrylic acids and a number of polysaccharides, both carboxylated and sulphated. It is concluded from this that the mechanism by which all of these materials are mucoadhesive is likely to be similar. For the mucoadhesive polymer Carbopol® 934P, it is demonstrated that the effect of PVP K30 is dependent on the concentration added. When tested in media of varying pH but constant ionic strength, 5% PVP K30 significantly reduces the adhesion in each case. When a number of polymers were included in mucoadhesive tablets, it was found that polyvinylpyrrolidones and polyoxyethylenes significantly reduce the observed adhesion, whereas soluble starch and polyvinylalcohol do not. Cumulative amounts of soluble starch, up to a concentration of 10%, did not significantly reduce the observed mucoadhesion. Insoluble or poorly soluble grades of polyoxyethylene and polyvinylpyrrolidone do not cause a significant reduction of observed mucoadhesion in the polymers tested. The common structural feature shared by polyvinylpyrrolidones and polyoxyethylenes is that they are both hydrogen bond acceptors for polyacrylic acid. It is proposed that these materials hinder the formation of the mucoadhesive bond between polymers and gastric tissue by preferentially hydrogen bonding to hydrated polymers and therefore reducing the strength of the bond between the mucoadhesive and mucin.
The Value of Information in a Sealed-Bid Auction (1981)

Abstract In this paper, we explore bidders' incentives to gather information in auctions, when there is one bidder with only public information and another with some private information. We find that the bidder with only public information makes no profit at equilibrium, while the bidder with private information generally makes positive profits. Moreover, the informed bidder's profits rise when he gathers extra information, and the increase in greater when the information is collected overtly than when it is collected covertly. When the uniformed bidder can observe some of the better-informed bidder's information, he prefers to make his observations covertly. If the seller has access to some of the better-informed bidder's information, or if he has affiliated information of his own, he can raise the expected price by adopting a policy of making that information public. However, there are cases where a policy of publicizing his information would lower the expected price. The distinguishing feature of these latter cases seems to be that the seller's information is complementary to the information of the better-informed bidder.