gebhart/patrepeval huggingface dataset:
Epigenetic Target Profiler: A Web Server to Predict Epigenetic Targets of Small Molecules (2021)

The identification of protein targets of small molecules is essential for drug discovery. With the increasing amount of chemogenomic data in the public domain, multiple ligand-based models for target prediction have emerged. However, these models are generally biased by the number of known ligands for different targets, which involves an under-representation of epigenetic targets, and despite the increasing importance of epigenetic targets in drug discovery, there are no open tools for epigenetic target prediction. In this work, we introduce Epigenetic Target Profiler (ETP), a freely accessible and easy-to-use web application for the prediction of epigenetic targets of small molecules. For a query compound, ETP predicts its bioactivity profile over a panel of 55 different epigenetic targets. To that aim, ETP uses a consensus model based on two binary classification models for each target, relying on support vector machines and built on molecular fingerprints of different design. A distance-to-model parameter related to the reliability of the predictions is included to facilitate their interpretability and assist in the identification of small molecules with potential epigenetic activity. Epigenetic Target Profiler is freely available at http://www.epigenetictargetprofiler.com.
Dimethylsulfoxidepentaammineruthenium(II) Hexafluorophosphate. A Spectroscopic Study (1971)

The infrared spectra of [Ru(NH 3 ) 5 (CH 3 ) 2 SO]X 2 , [Ru(ND 3 ) 5 (CH 3 ) 2 SO]X 2 , [Ru(NH 3 ) 5 (CD 3 ) 2 SO]X 2 , and [Ru(ND 3 ) 5 (CD 3 ) 2 SO]X 2 where X = PF 6 − have been examined in detail between 4000–200 cm −1 . These data, together with the 1 H n.m.r. spectrum of [Ru(NH 3 ) 5 (CH 3 ) 2 SO](PF 6 ) 2 in D 2 O, suggest that dimethyl sulfoxide is bonded to ruthenium via the sulfur atom in spite of the fact that the ν so frequency is not very different from that observed for uncoordinated dimethyl sulfoxide.
Nuclear targeting of plasmid DNA in human corneal cells (1999)

These results demonstrate that primary, non-transformed human corneal epithelial cells and keratocytes display sequence-specific nuclear import of plasmid DNA in the absence of mitosis. The small sequence that mediates nuclear localization of plasmids is active both in microinjected and cationic liposome transfected cells, and leads to increased gene expression. Thus, inclusion of this DNA sequence into non-viral vectors should improve the efficiency of ocular gene transfer in vivo.
Malignant and transforming activity of rous sarcoma virus. I. Malignant effect of rous sarcoma virus (1969)

Abstract Cultures of cells from embryos of Af, C3H‐H p/2 and (CBAT6T6 × Af)F 1 mice rapidly developed oncogenicity for syngeneic animals after exposure to RSV (Carr‐Zilber strain). The tumours of mice were virogenic and contained the group‐specific antigen of avian sarcoma‐leukosis complex. However, when the infected cells became transformed in morphology, they lost their oncogenicity for syngeneic animals.
Fiber optic sensor for substrate temperature monitoring (1990)

The use of an optical fiber Fabry–Perot interferometric temperature sensor for monitoring substrate temperature in a rf sputtering system is demonstrated. The sensor head consists of a continuous length of single mode silica fiber which contains two internal mirrors a distance of 1.08 cm apart to form the interferometer cavity. The laser light source for the sensor is located outside the vacuum system and connected to the sensor head via a fiber optic feedthrough. The accuracy of the sensor was 0.05 °C in this experiment, but considerable improvement is possible with better signal averaging techniques. The fiber optic sensor provided substrate temperature information during rf plasma excitation, when a nearby thermocouple ceased to function due to electromagnetic interference.
In Search of the Waterless Fracture (2013)

Waterless Fractures The first hydraulic fracture experiment was waterless. A gasoline gel was injected into the Hugoton field in 1947. What was once an emerging technology in the US has become the growth engine for oil and gas production globally, and the napalm-based mix that was used then looks like an anachronism. But fracturing using hydrocarbons is on the short list of options for the industry, which is looking for an effective substitute for water in hydraulic fracturing. Environmental questions have arisen about water use and water quality in unconventional resource development, which requires millions of gallons of water per well to open path-ways for oil and gas trapped in nearly impermeable rock. The Research Partnership to Secure Energy for America (RPSEA) has one waterless project in progress—to see if liquid nitrogen can fracture effectively—and the government/industry-funded research group is seeking more projects that experiment with waterless alternatives. “Water does work and has opened up the shale resources,” said Kent Perry, vice president of onshore programs at RPSEA. “(Fracturing) does take a lot of water. If you are in an area, particularly in parts of south Texas that are in a drought, even a little water is precious.” Another driver for seeking waterless fractures is the search for a way to pro-duce more of the oil and gas out of the ground. Oil recovery in unconventional formations is generally well below that of conventional formations, with 3% to 6% estimated ultimate recovery rates in many unconventional oil formations. “If you recover 10% (of the oil and gas), you are doing well but you are leaving 90% behind,” Perry said. “It is not just the fracture treatment. The whole approach will have to be looked at within those resources.” Waterless fracturing could also remove an impediment to tapping unconventional formations in many spots around the world: limited water supplies. During a panel discussion at the recent International Petroleum Technology Conference, Peter Voser, chief executive officer of Shell Oil, said he “told the R&amp;D group to come back with the waterless fracture.” His comment was delivered in Beijing, where Shell has been aggressively pursuing unconventional exploration opportunities in a country that has both enormous unconventional natural gas reserves and water shortages over large areas.
Micromotion at the Bone-Stem Interface during the Gait Cycle after Cementless Total Hip Replacement: Influence of Stem Design and Loading Level (1996)

The micromotion distribution of a cementless stem relative to femoral bone and the stress transfer were calculated with a three dimensional model including bone non-homogeneity, anisotropy and discontinuity of the bone-implant interface. Two implant designs (anatomical, straight) were investigated to point out the geometry effects. Micromotion distributions were calculated over the entire interface during a complete gait cycle taking into account the hip musculature forces. Different loading levels (from 20% to 100% of total load) were stimulated. For the two implants, peak values of distractive and shear micromotions were maximal at the Single Limb Stance phase. The implant geometry had no sensible effects on distractive micromotion magnitude. Conversely, the implant design had noticeable influences on shear micromotions. Regarding the effects of loading levels, at 20% of the full load, interface shear micromotions were lower than 30μm over the entire interface allowing bony ingrowth and expected to ensure initial stability for both implants. At 40%, shear micromotions exceeding 30μm appeared and were located differently according to the stem design.
High spin current density in gate-tunable spin-valves based on graphene nanoribbons (2023)

The usage of two-dimensional (2D) materials will be very advantageous for many developing spintronic device designs, providing a superior method of managing spin. Non-volatile memory technologies, particularly magnetic random-access memories (MRAMs), characterized by 2D materials are the goal of the effort. A sufficiently large spin current density is indispensable for the writing mode of MRAMs to switch states. How to attain spin current density beyond critical values around 5 MA/cm<sup>2</sup> in 2D materials at room temperature is the greatest obstacle to overcome. Here, we first theoretically propose a spin valve based on graphene nanoribbons (GNRs) to generate a huge spin current density at room temperature. The spin current density can achieve the critical value with the help of tunable gate voltage. The highest spin current density can reach 15 MA/cm<sup>2</sup> by adjusting the band gap energy of GNRs and exchange strength in our proposed gate-tunable spin-valve. Also, ultralow writing power can be obtained, successfully overcoming the difficulties traditional magnetic tunnel junction-based MRAMs have faced. Furthermore, the proposed spin-valve meets the reading mode criteria and the MR ratios are always higher than 100%. These results may open the feasibility avenues for spin logic devices based on 2D materials.
Evidence for a stem-cell lineage in corneal squamous cell carcinoma using synchrotron-based Fourier-transform infrared microspectroscopy and multivariate analysis (2010)

The cornea is one of the few human tissues where the in situ locations of stem cells (SCs), transient-amplifying (TA) cells and terminally-differentiated (TD) cells have been relatively well localised and characterised. Mid-infrared (IR) (4000-400 cm(-1)) is absorbed by biological molecules and facilitates the acquisition in the biochemical-cell fingerprint region (1800-900 cm(-1)) of spectra representative of structure and function. Human cornea derived from normal or squamous cell carcinoma (SCC) samples were acquired, cryosectioned (10 µm), floated onto BaF(2) windows and interrogated using synchrotron-based radiation (SRS) Fourier-transform IR (FTIR) microspectroscopy. Spectra were analysed using principal component analysis (PCA) with or without linear discriminant analysis (LDA) to allow cluster analysis of the cell categories. A clear cell lineage emanating from SCs to TA cells to TD cells was noted in normal samples. Within the SCC samples, a small sub-population of the cell-derived spectra pointed to a SC-like phenotype with the vast majority pointing to a TA cell-like character; these cells would tend to be the most proliferative within a tissue. Our findings suggest that SRS FTIR microspectroscopy has the potential to identify and characterise cancer SCs.
A metal-amorphous silicon-germanium alloy Schottky barrier for infrared optoelectronic IC on glass substrate application (1992)

The effects of material and structure parameters on an amorphous-silicon-germanium alloy Schottky barrier diode's responsivity have been investigated in detail. The effects contradict each other. A compromise is made in selecting parameters for construction of a Si/sub 1-x/Ge/sub x/:H Schottky barrier for an IR detector. The optimized amorphous-silicon-germanium alloy Schottky diode using x=0.43 alloy with a 900-nm-thick i-layer was found to have a peak at 850 nm with a responsivity of 0.6 A/W under -2-V bias. The diode also has a response time of 33 mu s and slight photodegradation. Thus, the diode becomes a candidate for manufacturing the infrared OEIC (optoelectronic integrated circuit) on glass substrate in applications which require size, reproducibility, and low cost more than sensitivity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Monte Carlo study of the impact of phosphor optical properties on EPID imaging performance (2018)

We have developed a Monte Carlo computational model of a clinically employed electronic portal imaging device (EPID), and demonstrated the impact of phosphor optical properties on the imaging performance. The EPID model was built with Geant4 application for tomographic emission. Both radiative and optical transport were included in the model. Modulation transfer function (MTF), normalized noise-power spectrum times the incident x-ray fluence (qNNPS), and detective quantum efficiency (DQE) were calculated for simulated and measured data, and their agreement was quantified by the normalized root-mean-square error (NRMSE). MTF was computed using a 100 µm wide slit tilted by 1.5° and qNNPS was estimated using the Fujita-Lubberts-Swank method. DQE was calculated from MTF and qNNPS data. The NRMSE value was 0.0467 for MTF, 0.0217 for qNNPS, and 0.0885 for DQE, showing good agreement between measurement and simulation. Five major optical properties, phosphor grain size, phosphor thickness, phosphor refractive index, binder refractive index, and packing ratio were tested for their influence on the qNNPS, MTF, and DQE(0) of the model. Generally, the effect on the qNNPS is greater than MTF, and no impact on DQE(0), except from phosphor thickness, was observed. Multiple applications, such as imager design optimization and investigations of the dosimetric performance, are expected to benefit from the validated model.
Sequence variations inOsAGPasesignificantly associated with amylose content and viscosity properties in rice (Oryza sativaL.) (2012)

Sequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativa L.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. An ADP-glucose pyrophosphorylase small unit 1 (OsAGPS1) SNP (A-G) was significantly associated with increased AC (P<0·001, R(2)=15·6%), while a 12-bp deletion of AGPase large unit 4 (OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (P<0·001, R(2)=16·6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.
Abstract 266: Effects Of Carotid Body Tumor Resection On Blood Pressure (2014)

Introduction: Removal of carotid body (CB) improves rodent models of HTN and HF, presumably via withdrawal of chemoreflex-induced sympathetic activation. CB tumor (CBT) resection abolishes the chemoreflex in humans and is associated with opposing effects on sympathetic regulation by accompanying damage of the baroreflex. The net effect of CBT removal on BP in subjects with pre-existent HTN is unknown. Methods: Retrospective analysis of 134 patients with uni- or bilateral CBT resection between 1990-2012. Twenty subjects met HTN entry criteria (BP≥140/90 mmHg or use of antihypertensive drugs) but two were excluded from analyses because of inadequate data. BP changes were assessed by a) acute ΔSBP: the change from the average SBP for the 3 months preceding surgery to the first reading after 30 days from the procedure, and b) chronic: the slope of the regression of SBP on time over the entire follow up, expressed as ΔSBP/year. BP changes were adjusted with covariate analyses. Covariates for acute ΔSBP were: the interval between pre and post BP readings and the change in therapy during this interval (assessed by a score of medications based on equipotency). Covariates for chronic ΔSBP were: total duration of follow-up, number of SBP readings and change in therapy during the entire period of study. Results: Age and duration of HTN were 56±4 and 10±4 years, respectively. There was a significant relationship between acute ΔSBP and the chronic slopes (r=0.47, p&lt;0.05) indicating that initial BP responses to CBT removal tend to be sustained. The univariate relationship showed that for every change of 0.4 mmHg in acute ΔSBP, there was a concomitant 1 mmHg/yr change in the chronic slope. Thirteen subjects (72%) had concordant reductions of ΔSBP and slope of any magnitude. In 6 subjects (33%), acute ΔSBP was ≥ -10 mmHg (corresponding to concomitant slopes ≥ 5.9 mmHg/yr). Conclusions: This is the first study to show that CBT removal is associated with a sustained reduction of BP in a subset of patients with comorbid HTN. Also, concomitant baroreceptor damage by CBT removal most likely leads to underestimation of the depressor effect of chemoreflex disruption. Development of a targeted removal of CB chemoreflex may conceivably have a role in the therapy of human hypertension.
Enterotoxins can support CAR T cells against solid tumors (2019)

Responses of solid tumors to chimeric antigen receptor (CAR) T cell therapy are often minimal. This is potentially due to a lack of sustained activation and proliferation of CAR T cells when encountering antigen in a profoundly immunosuppressive tumor microenvironment. In this study, we investigate if inducing an interaction between CAR T cells and antigen-presenting cells (APCs) in lymphoid tissue, away from an immunosuppressive microenvironment, could enhance solid-tumor responses. We combined CAR T cell transfer with the bacterial enterotoxin staphylococcal enterotoxin-B (SEB), which naturally links a proportion of T cell receptor (TCR) Vβ subtypes to MHC-II, present on APCs. CAR T cell proliferation and function was significantly enhanced by SEB. Solid tumor-growth inhibition in mice was increased when CAR T cells were administered in combination with SEB. CAR T cell expansion in lymphoid tissue was demonstrated, and inhibition of lymphocyte egress from lymph nodes using FTY720 abrogated the benefit of SEB. We also demonstrate that a bispecific antibody, targeting a c-Myc tag on CAR T cells and cluster of differentiation 40 (CD40), could also enhance CAR T cell activity and mediate increased antitumor activity of CAR T cells. These model systems serve as proof-of-principle that facilitating the interaction of CAR T cells with APCs can enhance their ability to mediate antitumor activity.
Outcomes of Liver Transplantation in 490 Patients with Hepatocellular Carcinoma: Validation of a Uniform Staging after Surgical Treatment (2007)

The AJCC/UICC staging system provides the best stratification of prognosis for patients undergoing liver transplantation for hepatocellular carcinoma. This confirms previous analyses in patients treated with hepatic resection. The AJCC/UICC staging system should be considered for uniform prediction of outcomes after surgery for hepatocellular carcinoma.
New Synthesis of Macrolide Pheromones of the Flat Grain Beetle,Cryptolestes pusillusSchönherr (1986)

(Z)-3-Dodecen-12-olide 1 and (5Z,13S)-5-tetradecen-13-olide 2, the macrolide pheromones of the flat grain beetle, were synthesized by employing the acetylene zipper reaction in the key steps.
Ecological dynamics of the bivalve‐killing dinoflagellate Heterocapsa circularisquama and its infectious viruses in different locations of western Japan (2007)

We studied the ecological relationships between the bloom-forming dinoflagellate Heterocapsa circularisquama and its infectious viruses in field surveys conducted in western Japan. The occurrence of H. circularisquama blooms in Imari Bay during 2002 and in Ago Bay during 2002 and 2004 was accompanied by specific increase in abundance of viruses lytic to H. circularisquama. Using northern dot-blot analysis, approximately 96% of the clonal virus isolates collected in the field surveys positively reacted with a molecular probe specific for HcRNAV (H. circularisquama RNA virus); hence, viral impacts on H. circularisquama population observed in these field surveys are considered largely due to HcRNAV and/or its closely related viruses. The dynamics of type UA viruses and type CY viruses having complementary host ranges to H. circularisquama clones were different in each survey and considered to reflect fluctuations in abundance of their suitable host cells in situ. The dynamics of H. circularisquama and its viruses in Ago Bay from 2002 to 2004 suggests the concentration of HcRNAV in the sediment prior to the host's blooming season is a significant factor in determining the size and length of the H. circularisquama blooms. These results support the hypothesis that HcRNAV infection is one of the significant factors affecting the population dynamics of H. circularisquama in both quantity (biomass) and quality (clonal composition).
Cancer pain: Beyond the ladder (1998)

Current estimates indicate that between 50 and 90% of patients with cancer experience pain. The World Health Organization has outlined a three-step analgesic ladder, that, if followed will result in close to 90% pain relief. Opioids should not be withheld for fear of addiction or respiratory depres sion and are clearly the most effective systemic analgesic available for patients with cancer-related pain. Unfortunately, opioids can also cause side effects including, but not limited to, constipation and mental cloudiness. Interventional therapies and physical modalities can decrease pain without systemic side effects associated with opioids and should be considered a useful adjunct in the battle against pain. It is likely that by incorporating interventional and non-pharmacologic approaches, the success rate of pain control and the quality of life can be improved.
13C NMR chemical shifts of 2,4,5,‐ tri‐substituted 2H‐pyridazin‐3‐ones (1990)

Abstract The 13 C NMR spectra of a series of 2‐X‐4‐Y‐5‐Z‐substituted 2H‐pyridazin‐3‐ones were measured and assigned on the basis of results from one‐dimensional semi‐selective INEPT or one‐dimensional relayed coherence transfer (HICUUP) experiments.
Development of an Energy-Sensitive Detector for the Atom Probe Tomography (2021)

A position and energy-sensitive detector has been developed for atom probe tomography (APT) instruments in order to deal with some mass peak overlap issues encountered in APT experiments. Through this new type of detector, quantitative and qualitative improvements could be considered for critical materials with mass peak overlaps, such as nitrogen and silicon in TiSiN systems, or titanium and carbon in cemented carbide materials. This new detector is based on a thin carbon foil positioned on the front panel of a conventional MCP-DLD detector. According to several studies, it has been demonstrated that the impact of ions on thin carbon foils has the effect of generating a number of transmitted and reflected secondary electrons. The number generated mainly depends on both the kinetic energy and the mass of incident particles. Despite the fact that this phenomenon is well known and has been widely discussed for decades, no studies have been performed to date for using it as a means to discriminate particles energy. Therefore, this study introduces the first experiments on a potential new generation of APT detectors that would be able to resolve mass peak overlaps through the energy-sensitivity of thin carbon foils.