gebhart/patrepeval huggingface dataset:
Chromatin Isolation by RNA Purification (ChIRP) (2012)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression (1,2,3,4,5,6,7). The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion (8,9). While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation (10,11). However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide( 3,12,13), but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex (14); HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex (13). Prior studies mapping RNA occupancy at chromatin have revealed substantial insights (15,16), but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution (17). This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. ChIRP is applicable to many lncRNAs because the design of affinity-probes is straightforward given the RNA sequence and requires no knowledge of the RNA's structure or functional domains.
Corrosion and Scaling Monitoring under Real Downhole Conditions in Sour Gas Wells (2018)

Abstract One of the major challenges of corrosion and scaling management in sour gas wells is to effectively monitor corrosion and scaling under real-flow regime conditions. It is very difficult to simulate the actual environment and flow conditions in laboratory experiments to study downhole corrosion and scale formation. Understanding the corrosion and scaling mechanism under downhole conditions is very important in order to develop effective prevention and mitigation strategies in a timely manner. An advanced downhole corrosion and scale monitoring (DCSM) tool has been designed and developed to monitor corrosion and scale formation in sour gas wells. This monitoring system represents significant improvements over the current industrial technology by directly measuring corrosion and scale deposition in real downhole conditions using exchangeable coupons with identical metallurgy as the downhole completion tubing. A slick line with a retrievable high-expansion gauge hanger was used to deploy and anchor the DCSM downhole at the desired depth. The tool was retrieved after 3 months exposure to the reservoir conditions for post-laboratory analysis. Advanced analytical techniques were carried out to understand the corrosion and scaling mechanism, including SEM, EDS, XRD, and surface profile measurement besides quantifying the weight changes. The results showed that a thin layer (~3-4 μm in thickness) of iron sulfide scale was deposited on the surface of coupon. It served as a protective layer to prevent and reduce further corrosion and scale buildup. To understand the mechanisms of scaling, the surface scale deposit was removed by corrosion inhibited acidic solution. The surface profile measurement showed localized pitting corrosion which appeared on the surface of coupon, which indicates that corrosion happened first followed by scale layer deposition on metal coupon surface. The newly developed DCSM tool has an advanced design which allows direct corrosion and scaling monitoring under downhole conditions. Post-laboratory analysis on retrieved coupons can provide corrosion and scaling mechanism for specific metallurgy under real downhole conditions. Proper corrosion and scale management programs could be designed to minimize the effects of corrosive gases. The developed tool can be used to monitor the effectiveness of the corrosion treatment and can be deployed in sweet gas wells, oil wells and water supplier wells.
First example of high loaded polymer-stabilized nanoclusters immobilized on hydrotalcite: effects in alkyne hydrogenation (2004)

Poly(N-vinyl-2-pyrrolidone)-stabilized Pd-nanoclusters, for the first time exclusively supported on the hydrotalcite lateral surface, showed a remarkable catalytic performance in the selective hydrogenation of 3-hexyn-1-ol, which can be ascribed to both the influence of the protecting polymer PVP as well as the nature of the support.
Field Applications of Steam Foam for Mobility Improvement and Profile Control (1996)

Summary Foams are used to control and improve the injection profile in secondary or tertiary gas-injection processes and reduce gas mobility far from the injectors. Over the last decade, significant progress has been made in the understanding of the complex foam processes in porous rocks. The goal of this paper is to review consistently, albeit somewhat subjectively, several important field tests of foams, compare their performance, and critically evaluate the economic benefits from foam injection. It is shown that early, transient, and usually small oil production responses to surfactant injection are real, and depend critically on the reservoir architecture and gas flood implementation. These early production responses are related to the improvements of gas-injection profile by foam and are often quite profitable. The delayed, but bigger oil production responses are caused by foam propagation into the reservoir and could be very profitable, depending on the injection policy. An outline of an ideal future foam pilot is presented, and important advances in rigorous modeling of foam processes are discussed.
Improvement of defocus tolerance in a half-micron optical lithography by the focus latitude enhancement exposure method: Simulation and experiment (1989)

The new method for enhancing the focus latitude in optical lithography, named FLEX (focus latitude enhancement exposure) has been investigated. In FLEX the imaging characteristics are greatly affected by several key parameters such as distance between adjacent focal planes and illuminator coherence factor. The effect of these parameters on optical image characteristics have been examined using computer simulations. The results of the simulations have been verified by applying FLEX to imaging of sub-half-micron patterns using a high numerical aperture i-line stepper. This has confirmed the validity of FLEX in delineating feature sizes in the order of 0.3∼0.5 μm. In particular, the depth of focus for hole patterns is found to be increased more than ten times, if necessary, with no degradation in resolution. However, the high-contrast resist process is necessary in applying FLEX to patterns like L/S. FLEX will be a great help to future optical lithography with high NA and/or short wavelength optical systems.
Orbital Fibroblast Heterogeneity May Determine the Clinical Presentation of Thyroid-Associated Ophthalmopathy (2002)

Thyroid-associated ophthalmopathy, a process in which the orbital tissues become inflamed and are remodeled, occurs with a variable presentation. In some patients, eye muscle enlargement predominates. In others, the connective/adipose tissue enlargement appears the more significant problem. Orbital fibroblasts exhibit heterogeneous phenotypes in culture. Here we report that fibroblasts derived from the connective/adipose tissue depot are distinct from those investing the extraocular muscles. Connective tissue fibroblasts represent a bimodal population of cells with regard to the surface display of the glycoprotein, Thy-1. Perimysial fibroblasts in contrast express Thy-1 uniformly. In that regard, they resemble those from the skin. When subjected to a newly defined set of culture conditions, adipocyte differentiation occurs in up to 43% of the cells. All adipocytes examined failed to display Thy-1. Fibroblasts derived from perimysium and dermis uniformly do not differentiate into adipocytes when incubated under identical culture conditions. Both Thy-1+ and Thy-1− connective tissue fibroblasts express the adipogenic trigger, peroxisome proliferator activator γ, suggesting that differences in the potential for differentiation may reside with phenotypic attributes downstream from this receptor/adipogenic transcription factor. These observations enhance our understanding of orbital adipogenesis and define previously unrecognized differences between fibroblasts from the extraocular muscle and connective tissue.
Reinforcement Learning for Learning Rate Control (2017)

Stochastic gradient descent (SGD), which updates the model parameters by adding a local gradient times a learning rate at each step, is widely used in model training of machine learning algorithms such as neural networks. It is observed that the models trained by SGD are sensitive to learning rates and good learning rates are problem specific. We propose an algorithm to automatically learn learning rates using neural network based actor-critic methods from deep reinforcement learning (RL).In particular, we train a policy network called actor to decide the learning rate at each step during training, and a value network called critic to give feedback about quality of the decision (e.g., the goodness of the learning rate outputted by the actor) that the actor made. The introduction of auxiliary actor and critic networks helps the main network achieve better performance. Experiments on different datasets and network architectures show that our approach leads to better convergence of SGD than human-designed competitors.
First-Principles Study of the Graphene@MoSe<sub>2</sub> Heterobilayers (2011)

Very recently, the graphene@MoSe2 heterobilayers [G@MS HBLs] were successfully synthesized experimentally. In this work, the adhesion and electronic properties of the G@MS HBLs have been studied by using density functional theory. It is found that the graphene is weakly bound to the MoSe2 monolayer without any site selectivity. The bands of G@MS HBLs have characteristic graphene-like features with a small band gap (2 meV) opening at K. However, the gap value is significantly lower than kBT at room temperature and can even vanish at room temperature, which suggests that the unusual electronic properties of graphene in G@MS HBLs are comparable to those in the free-standing graphene. Thus, the MoSe2 monolayer might be considered as a promising substrate for potential graphene-based devices. The physical origin of the semiconducting property is related to the inhomogeneity of the onsite energy of C atoms induced by MoSe2. Our results provide a detailed understanding of the interfacial properties of G@MS HBLs and help to predict the performance of graphene-based nanoelectronics and nanocomposites.
IL-7 sustains CD31 expression in human naive CD4+ T cells and preferentially expands the CD31+ subset in a PI3K-dependent manner (2008)

The CD31(+) subset of human naive CD4(+) T cells is thought to contain the population of cells that have recently emigrated from the thymus, while their CD31(-) counterparts have been proposed to originate from CD31(+) cells after homeostatic cell division. Naive T-cell maintenance is known to involve homeostatic cytokines such as interleukin-7 (IL-7). It remains to be investigated what role this cytokine has in the homeostasis of naive CD4(+) T-cell subsets defined by CD31 expression. We provide evidence that IL-7 exerts a preferential proliferative effect on CD31(+) naive CD4(+) T cells from adult peripheral blood compared with the CD31(-) subset. IL-7-driven proliferation did not result in loss of CD31 expression, suggesting that CD31(+) naive CD4(+) T cells can undergo cytokine-driven homeostatic proliferation while preserving CD31. Furthermore, IL-7 sustained or increased CD31 expression even in nonproliferating cells. Both proliferation and CD31 maintenance were dependent on the activation of phosphoinositide 3-kinase (PI3K) signaling. Taken together, our data suggest that during adulthood CD31(+) naive CD4(+) T cells are maintained by IL-7 and that IL-7-based therapies may exert a preferential effect on this population.
Phase II study of chidamide in combination with cisplatin in patients with metastatic triple-negative breast cancer (2021)

The addition of chidamide did not improve the efficacy of cisplatin in the first-line treatment against advanced TNBC; thus, the phase II clinical trial did not progress any further. Our study appears to be the first to investigate the HDAC inhibitor in TNBC patients and showed disappointing results, which should inform future studies. Future research on cisplatin-based combination treatments for TNBC should consider selecting patients based on predictive biomarkers to increase the clinical benefits.
Layered and Homogeneous Films of Aluminum and Aluminum/Silicon with Titanium and Tungsten for Multilevel Interconnects (1985)

Layered structures and homogeneous alloy films synthesized by sputter deposition were investigated for use in a VLSI multilevel interconnect technology. Major areas studied include hillock formation, resistivity before and after annealing, film composition and structure, reproducibility, interlevel shorts, and dry etching. It has been demonstrated in this work that aluminum alloyed with silicon and titanium and layered with titanium offers advantages over current technological materials for interconnections in integrated circuits. Measurements of surface roughness and electrical shorts between two levels of metal showed that the hillock densities in the films are significantly reduced when small amounts (one to three atomic percent) of titanium and silicon are present. The resistivity of such homogeneous films, however, is 4.5 to 5.5 /spl mu//spl Omega//spl dot/cm, which is higher than standard metallization alloys. When Al/Si was layered with Ti, no hillocks were observed and the resistivity of the composite films was comparable to standard metallization alloys.
5-Lipoxygenase and 5-Lipoxygenase Activating Protein (FLAP) Immunoreactivity in Lungs from Patients with Primary Pulmonary Hypertension (1998)

Inflammatory infiltrates and endothelial cell proliferation have been appreciated in plexiform and concentric lesions, which characterize the vascular remodeling in primary pulmonary hypertension (PPH). Leukotriene production by perivascular and alveolar macrophages relies on activation of 5-lipoxygenase (5-LO), with translocation of the enzyme to the nuclear membrane, and association with the 5-LO activating protein (FLAP). Using immunohistochemical staining, we localized and semi-quantitatively estimated the abundance of 5-LO and FLAP in lungs obtained from patients with PPH, patients with interstitial lung disease (ILD), and normal control subjects. Expression of 5-LO and FLAP was prominent in alveolar macrophages in both the normal and PPH lungs; however, alveolar macrophages were more frequently clustered in the vicinity of remodeled blood vessel in PPH. Medium- and small-size pulmonary arteries in PPH showed more abundant FLAP expression than in control and ILD lungs. 5-LO expression in small arteries in PPH was more intense than in control and ILD patients. Endothelial cells in plexiform and concentric lesions in PPH expressed both 5-LO and FLAP. In situ hybridization confirmed the presence of 5-LO transcripts in macrophages and endothelial cells of the remodeled vessels in PPH. We propose that the overexpression of 5-LO and FLAP represents evidence for the participation of inflammation in the process of PPH vasculopathy or, alternatively, that the overabundance of the enzymes involved in generation of inflammatory mediators may themselves be related to vascular cell proliferation and cell growth.
Continuous interleukin-2 and lymphokine-activated killer cells for advanced cancer: a National Biotherapy Study Group trial. (1991)

We conducted a multicenter, phase II trial of continuous-infusion recombinant interleukin-2 (rIL-2) and lymphokine-activated killer (LAK) cells. Patients had advanced cancer, measurable disease, and a good performance level. Treatment included a 5-day continuous infusion of 18 x 10(6) IU/m2/d of rIL-2 followed by 1 day of rest, 4 days of leukapheresis to collect cells for in vitro augmentation of cellular cytotoxicity, and 5 more days of rIL-2 infusion with reinfusion of LAK cells for 3 successive days. Therapy was repeated after 2 weeks. There were 117 patients enrolled: 63% were males, with a median age of 51 years. Eighty-two percent were managed in oncology units, and 18% were in intensive care units. Six patients died within 1 month of initiating therapy. In renal cell carcinoma, the response rate was one of 31 patients (3%), with a median survival of 10.7 months. In melanoma, the response rate was four of 33 patients (12%), with a median survival of 6.1 months. For all other histologies, response rate was three of 53 patients (5%), with a median survival of 7.4 months. All responders were asymptomatic when therapy was initiated. This trial confirms the feasibility of administering continuous rIL-2 and LAK cells outside the intensive care unit environment. Antitumor activity in melanoma was similar to that seen in multicenter trials of bolus rIL-2 and LAK cells. Activity in renal cell cancer was disappointing.
Electroless Copper Deposition in a Blind Via Hole of Printed Wiring Board. Uniform Copper Deposition by Axial Temperature Gradient (2000)

Electroless copper deposition on the wall of the blinda holes was numerically simulated by solving a conventional diffusion equation with the reduction reaction of copper(II)on the wallHighly non-uniform copper deposition was ascribed to the small rate of copper(II)transport to the inmost part of the hole in comparison with the rate of the copper depositionparticularly in the cases of the aspect ratios of two or greaterAccording to the preliminary mns of the copper deposidonan applicadon ofthe u1asonicbraon at the deposidon step improved the unomity substantially but not very signicantlyHaving been expected the enhance(l trImsjer of copper(ID in the holetemperature gradient along the ads of the hole was applied in the simulation of the copper depositionwhich results suggested more unifoma copper deposition than in the isothermal conditionExperimentallycopper deposited preferentially rather at the inmost part of the hole under the conditions of298K at the hole opening and338K at the bottom It was found that the temperature gradient copper deposition on the wall of the blin(i via holes provides us with the unifbrm layer of coPPer PhntedWiringBoardElec01essCopperDeposidonBlindViaHoleUnomCopperDeposition
A new generator for ionic gallium-68. (1980)

To meet the needs created by the rapid development of positron tomographic techniques, a new Ge-68 leads to Ga-68 generator has been developed. By elution under reduced pressure, this tin dioxide/1 N HCl generator provides a sterile solution of Ga-68 in ionic form, ready for use in the preparation of many radiopharmaceuticals. Since the Ga-68 recovery yield is high (75--80%) and the elution time very short (less than 2 min), these products possess maximum activity. Owing to its very slight Ge-68 leakage (less than 0.0002% per elution), the tin dioxide/HCl generator is long-lasting and, more importantly, the radiotoxicity of the labeled derivatives is kept to a minimum. The ionic Ga-68 obtained in this way has been used to label several radiopharmaceuticals.
Pneumocystis carinii karyotypes (1990)

Pulsed-field gel electrophoresis techniques were used to examine the chromosomes of Pneumocystis carinii isolated from laboratory rats and two human subjects. P. carinii organisms isolated from each of four rat colonies and from two patients each produced a distinct band pattern, but in all cases the bands ranged in size from 300 to 700 kilobase pairs. P. carinii from three rat colonies produced patterns containing 15 prominent bands. Of these 15 bands, 2 stained more intensely than would be expected of bands of their size, suggesting that the P. carinii haploid genome contains 17 to 19 chromosomes. Summing the molecular sizes of the bands and accounting for staining intensities suggested that the haploid genome of rat-derived P. carinii contains on the order of 10(7) base pairs. Human-derived P. carinii produced patterns containing 10 to 12 bands which appeared to be similar to the 15-band patterns seen in rat-derived P. carinii with respect to the size range of the bands. P. carinii from the fourth rat colony produced a more complex band pattern containing approximately 22 bands, most of which appeared to comigrate with the bands present in one of the 15-band P. carinii patterns, suggesting that these animals were simultaneously infected by two different varieties of P. carinii. Hybridization experiments using oligonucleotide probes specific for the P. carinii 18S rRNA gene supported this possibility. The band pattern of P. carinii derived from a given rat colony was generally stable over time. P. carinii band patterns were not strictly rat strain specific and appeared to be transferrable between animals housed in the same room.
Addition Aware Quantization for Low Complexity and High Precision Constant Multiplication (2009)

Multiplication by constants can be efficiently realized using shifts, additions, and subtractions. In this work we consider how to select a fixed-point value for a real valued, rational, or floating-point coefficient to obtain a low-complexity realization. It is shown that the process, denoted addition aware quantization, often can determine coefficients that has as low complexity as the rounded value, but with a smaller approximation error by searching among coefficients with a longer wordlength.