gebhart/patrepeval huggingface dataset:
Abstract IA14: Functional genomics and cancer vulnerabilities (2014)

Abstract Recent advances in genomics now make it possible to consider enumerating all of the genetic lesions in specific cancers. These approaches will yield critical information regarding the identification, number, and types of alterations found in human tumors and are increasingly being applied prospectively to patient samples in the clinic. At the same time, complementary approach to decipher the molecular basis of malignant transformation depends upon the application of genome scale tools to annotate the function of genes involved in cancer initiation and progression. Over the past several years, we have developed genome scale RNAi libraries and open reading frame expression libraries that permit a systematic evaluation of genes involved in cancer initiation and maintenance. Using these libraries, we have now performed screens in a panel of human cancer cell lines to systematically identify cancer vulnerabilities. By combining these functional approaches with information derived from mapping the structural abnormalities present in cancer genomes, we have identified several new oncogenes that contribute to cancer development. The ability to systematically manipulate gene expression at genome scale now provides opportunities to investigate the function of genes involved in cancer initiation and maintenance, which will provide a framework for therapeutic strategies. Citation Format: William C. Hahn. Functional genomics and cancer vulnerabilities. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr IA14.
DISCREPANCY BETWEEN RENIN mRNA AND PLASMA RENIN LEVEL IN ANGIOTENSIN‐CONVERTING ENZYME INHIBITOR‐TREATED RATS (1993)

1. To investigate the role of transcriptional and post-transcriptional factors in increasing renin synthesis secondary to angiotensin-converting enzyme (ACE) inhibitors, we studied the changes in levels of renal renin mRNA, plasma renin and other hormonal factors. 2. Spontaneously hypertensive rats were orally administered 10 mg/kg spirapril or vehicle daily for 3, 14 or 28 days. 3. Plasma renin activity in the spirapril-treated group was significantly elevated compared with that in the vehicle group at any time (P < 0.01). However, there was no significant change in plasma angiotensin II concentration between the two groups. The ratio of renal renin mRNA to beta-actin mRNA in the spirapril-treated group was higher than that in the control group (P < 0.01). 4. At 28 days, plasma renin activity in the spirapril-treated group was significantly elevated compared with that at 14 days (P < 0.05). However, there was no change in renin mRNA between 14 and 28 days after ACE inhibitor administration. 5. Plasma ACE activity in the treatment group was less than that in the control group at any time (P < 0.01). 6. Our study demonstrated a non-proportional change in plasma renin and renal renin mRNA levels. It is suggested that the main determinant of the rate of renin synthesis after administration of an ACE inhibitor may be post-transcriptional factors, and that unknown mechanisms may be involved in the increase in plasma renin level after long-term administration of ACE inhibitor in addition to the short feedback mechanism brought about by the decrease in angiotensin II.
Consumption of fish oil high-fat diet induces murine hair loss via epidermal fatty acid binding protein in skin macrophages (2022)

Fats are essential in healthy diets, but how dietary fats affect immune cell function and overall health is not well understood. Mimicking human high-fat diets (HFDs), which are rich in different fatty acid (FA) components, we fed mice various HFDs from different fat sources, including fish oil and cocoa butter. Mice consuming the fish oil HFD exhibit a hair-loss phenotype. Further studies show that omega-3 (n-3) FAs in fish oil promote atypical infiltration of CD207<sup>-</sup> (langerin<sup>-</sup>) myeloid macrophages in skin dermis, which induce hair loss through elevated TNF-α signaling. Mechanistically, epidermal fatty acid binding protein (E-FABP) is demonstrated to play an essential role in inducing TNF-α-mediated hair loss by activating the n-3 FA/ROS/IL-36 signaling pathway in dermal resident macrophages. Absence of E-FABP abrogates fish oil HFD-induced murine hair loss. Altogether, these findings support a role for E-FABP as a lipid sensor mediating n-3 FA-regulated macrophage function and skin health.
Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy (2021)

Anti-PD-1 therapy is used as a front-line treatment for many cancers, but mechanistic insight into this therapy resistance is still lacking. Here we generate a humanized (Hu)-mouse melanoma model by injecting fetal liver-derived CD34<sup>+</sup> cells and implanting autologous thymus in immune-deficient NOD-scid IL2Rγ<sup>null</sup> (NSG) mice. Reconstituted Hu-mice are challenged with HLA-matched melanomas and treated with anti-PD-1, which results in restricted tumor growth but not complete regression. Tumor RNA-seq, multiplexed imaging and immunohistology staining show high expression of chemokines, as well as recruitment of FOXP3<sup>+</sup> Treg and mast cells, in selective tumor regions. Reduced HLA-class I expression and CD8<sup>+</sup>/Granz B<sup>+</sup> T cells homeostasis are observed in tumor regions where FOXP3<sup>+</sup> Treg and mast cells co-localize, with such features associated with resistance to anti-PD-1 treatment. Combining anti-PD-1 with sunitinib or imatinib results in the depletion of mast cells and complete regression of tumors. Our results thus implicate mast cell depletion for improving the efficacy of anti-PD-1 therapy.
SCHEME-FIELD MODELING OF THERMAL PROCESSES IN INDUCTION MOTORS (2017)

Purpose. Development of a new approach for increasing thermal calculations accuracy by thermal field and scheme combinating simulation in determining the effective heat conductivities in details and nodes of induction motor.Research methods: the heat conductivity theory, heat transfer, thermal equivalent circuit, thermal potentials, thermal field simulation, finite elements methods.The obtained results. The integrated method for conversion data of field modeling into thermal circuit model parameters is researched, which significantly reduces influence of nodes quantity of the thermal circuit on the accuracy of parameters determination by matrix invariancy of geometrical conductivities to temperature changes of heat conductivity values of induction motors constructional and active materials. By means of this method, for discretization induction motor spatial model on separate components, it is possible in advance to determine the components of matrix conductivities and to prevent the degeneration of this matrix in the scheme model.Scientific novelty. A new method of scheme model conversion with the use of an integral thermal potential is researched, which allows to pass from heat resistances, as a parameters of thermal equivalent circuit, to geometric conductivities of this scheme. It has been proved that by processing the data arrays of field modeling for determination geometric conductivities of thermal equivalent circuit, it is possible to prevent degeneration of matrix conductivities for the stationary thermal mode of induction motor in short-circuit mode, having provided reduction of nodes quantity and increase in computing efficiency and accuracy.Practical significance. The integrated method for converting data of induction motor field modeling into thermal model parameters allows at increase in the number of nodes in thermal scheme from one to ten to reduce the average value of a relative error from 9,2% to 2,42%, what completely meets requirements at designing of induction motors, and also for imitating modeling of thermal processes dynamics at the variable operating conditions.
Synthesis of 1,4:3,6‐Dianhydrohexitols Diesters from the Palladium‐Catalyzed Hydroesterification Reaction (2014)

The hydroesterification of alpha olefins has been used to synthesize diesters from bio-based secondary diols: isosorbide, isomannide, and isoidide. The reaction was promoted by 0.2% palladium catalyst generated in situ from palladium acetate/triphenylphosphine/para-toluene sulfonic acid. Optimized reaction conditions allowed the selective synthesis of the diesters with high yields and the reaction conditions could be scaled up to the synthesis of hundred grams of diesters from isosorbide and 1-octene with solvent-free conditions.
A View of Music (2015)

Inspired by the idea of synesthesia, or the intermingling of senses [10], we have developed an algorithm that transforms raw sound into a pictographic representation using the physics of a signal. We apply our method to music, the outcome of which is an animation that is not only synchronized with the music, but that mimics aspects of the music itself. We discuss the results of our concept and an implementation, which includes illustrations provided from a variety of music sources. As well, we provide our current parameterization technique and discuss the internal behaviors. We close with a discussion of perception, consonance, and dissonance, and a road-map for future work.
Impact of Landau Damping on Field Enhancement in Plasmonic Dimers (2017)

We show that Landau damping presents the most practically-relevant limit to the achievable plasmonic enhancement inside the narrow gaps of plasmonic dimers and other similarly-shaped plasmonic nanoantennas.
Differential Treatment for Stuff and Things: A Simple Unsupervised Domain Adaptation Method for Semantic Segmentation (2020)

We consider the problem of unsupervised domain adaptation for semantic segmentation by easing the domain shift between the source domain (synthetic data) and the target domain (real data) in this work. State-of-the-art approaches prove that performing semantic-level alignment is helpful in tackling the domain shift issue. Based on the observation that stuff categories usually share similar appearances across images of different domains while things (i.e. object instances) have much larger differences, we propose to improve the semantic-level alignment with different strategies for stuff regions and for things: 1) for the stuff categories, we generate feature representation for each class and conduct the alignment operation from the target domain to the source domain; 2) for the thing categories, we generate feature representation for each individual instance and encourage the instance in the target domain to align with the most similar one in the source domain. In this way, the individual differences within thing categories will also be considered to alleviate over-alignment. In addition to our proposed method, we further reveal the reason why the current adversarial loss is often unstable in minimizing the distribution discrepancy and show that our method can help ease this issue by minimizing the most similar stuff and instance features between the source and the target domains. We conduct extensive experiments in two unsupervised domain adaptation tasks, i.e. GTA5 → Cityscapes and SYNTHIA → Cityscapes, and achieve the new state-of-the-art segmentation accuracy.
Extended ultra-flat bands in photonic crystals (2005)

We create one-dimensional extended ultra-flat bands with relative frequency widths below 1% in two-dimensional photonic crystals. Caused by an interior saddle point, these flat bands lead to an enhanced density of states and improved self-collimation.
365. Long-Term Toxicology Evaluation of AAVrh. 10hARSA Administration to the CNS of Nonhuman Primates to Treat Metachromatic Leukodystrophy (2016)

Metachromatic leukodystrophy (MLD), a lysosomal storage disorder caused by the deficiency of the enzyme arylsulfatase A (ARSA), is a recessive, fatal neurodegenerative lysosomal storage disease associated with intracellular accumulation of sulfatides in the CNS. The disease is fatal, with no approved therapy. The focus of this study is to test the hypothesis that direct CNS administration of AAVrh.10hARSA (AAVrh.10 serotype vector coding for the human ARSA cDNA) to the CNS of nonhuman primates at doses scalable to humans has an acceptable long term safety profile. Safety of intraparenchymal administration of AAVrh. 10hARSA was evaluated following its administration to the CNS of non-human primates (NHPs, African Green monkeys, n=24) at 12 locations in the white matter centrum ovale at two different doses (total dose 2.85×1010 genome copies (gc), equivalent to human clinical dose of 2.85×1011 gc previously used via a similar route of administration in humans, and 1.5×1012 gc, a 1.7-log higher dose, equivalent to a human dose of 1.5×1013 gc). NHPs administered in a similar fashion with AAVNull vector (a vector with an expression cassette without a translatable sequence) and sham (PBS) were used as controls. Target locations were determined using CAT and MRI imaging. The groups (n=6/group) were sacrificed at 1, 13, 26, and 52 wk following vector administration to determine short and long-term effects of treatment. General safety, hematologic, serum chemistry and CNS histopathology parameters were assessed at several time points up to 1 yr after vector administration. Additional in-life safety assessments included behavioral videotaping and CNS monitoring by magnetic resonance imaging (MRI) at 13, 26, and 52 wk post-administration. The vector-administered groups did not differ from the controls in any parameter of general assessment or comprehensive blood profile (complete blood count, chemistry panel). Blinded videotape analysis of NHP behavior pre-surgery and post-administration showed no discernible neurological differences. No significant adverse effects were observed in animals treated with low dose AAVrh. 10hARSA; the only abnormal observation was presence of limited and reversible, minimal to mild T and B cell focal infiltrates at the CNS administration sites, findings that were corroborated by MRI. Animals treated with the higher dose of both the ARSA and Null vectors (1.5×1012 gc) demonstrated significant infiltrates of T cells, B cells and activated microglial cells and/or macrophages in the brain at the sites of administration. Similar observations were made from MRIs images, i.e., the higher dose may be associated with some local adverse effects, although these findings did not have clinical consequences on in-life data, complete blood count, serum chemistry or behavior in these NHPs. Together these findings demonstrate the safety of AAVrh.10hARSA administration at 2.85×1010 gc, equivalent to a human dose of 2.85×1011 gc and support the use of this vector as a vehicle for therapy of MLD.
Deletion at Fragile Sites Is a Common and Early Event in Barrett's Esophagus (2010)

Barrett's esophagus (BE) is a premalignant intermediate to esophageal adenocarcinoma, which develops in the context of chronic inflammation and exposure to bile and acid. We asked whether there might be common genomic alterations that could be identified as potential clinical biomarker(s) for BE by whole genome profiling. We detected copy number alterations and/or loss of heterozygosity at 56 fragile sites in 20 patients with premalignant BE. Chromosomal fragile sites are particularly sensitive to DNA breaks and are frequent sites of rearrangement or loss in many human cancers. Seventy-eight percent of all genomic alterations detected by array-CGH were associated with fragile sites. Copy number losses in early BE were observed at particularly high frequency at FRA3B (81%), FRA9A/C (71.4%), FRA5E (52.4%), and FRA 4D (52.4%), and at lower frequencies in other fragile sites, including FRA1K (42.9%), FRAXC (42.9%), FRA 12B (33.3%), and FRA16D (33.3%). Due to the consistency of the region of copy number loss, we were able to verify these results by quantitative PCR, which detected the loss of FRA3B and FRA16D, in 83% and 40% of early molecular stage BE patients, respectively. Loss of heterozygosity in these cases was confirmed through pyrosequencing at FRA3B and FRA16D (75% and 70%, respectively). Deletion and genomic instability at FRA3B and other fragile sites could thus be a biomarker of genetic damage in BE patients and a potential biomarker of cancer risk.
Vacuum ultraviolet emission characteristics from He–Ne–Xe gas discharge in an alternating current plasma display panel cell (2000)

We measured the time integrated vacuum ultraviolet (VUV) emission spectra of He–Ne–Xe gas mixture from a surface type alternating current (ac) plasma display panel cell. The measured emission lines are the resonance line (147 nm) from Xe*(1s4), the first continuum (150 nm) and the second continuum (173 nm) from Xe dimer excited states. The relative intensities of VUV spectral lines from Xe* and Xe2* are dependent on the He/Ne mixing ratio as well as the Xe partial and total pressure. The intensity of 147 nm VUV increases with the Ne content increase and Xe2* molecular emission increases with the He content increase. Infrared (IR) spectra and the time variation of VUV were measured to explain the reaction pathway and the effect of the mixing ratio of He/Ne on the spectral intensity. A detailed study for the decay time shows that the decay time of 147 nm has two time constants and the radiation of 150 and 173 nm results mainly from Xe*(1s5). The IR spectra shows that the contribution from Xe**(&amp;gt;6 s) to Xe*(1s5) and Xe*(1s4) in He–Xe is different from that of Ne–Xe. The change of IR intensity explains the spectral intensity variations of He–Xe and Ne–Xe discharge.
IP flow mobility: smart traffic offload for future wireless networks (2011)

The recent proliferation of smartphone-based mobile Internet services has created an extraordinary growth in data traffic over cellular networks. This growth has fostered interest in exploring alternatives to alleviate data congestion while delivering a positive user experience. It is known that a very small number of users and applications cause a big percentage of the traffic load. Hence, adopting smarter traffic management mechanisms is one of the considered alternatives. These mechanisms allow telecom operators to move selected IP data traffic, for instance, between the cellular infrastructure and the WLAN infrastructure, which is considered a key feature in the latest 3GPP and IETF specifications. This article presents and compares two possible approaches to IP flow mobility offloading that are currently being considered by the IETF. The first one is based on extending existing client-based IP mobility solutions to allow flow mobility where the user terminal is fully involved in the mobility process, and the second one is based on extending current network- based IP mobility solutions where the user terminal is not aware of the mobility.
Bio‐inspired Micropatterned Platform to Steer Stem Cell Differentiation (2011)

Controlled stem cell differentiation on micropatterned biodegradable substrates involves modulation of the canonical FAK–ERK (focal adhesion kinase–extracellular-signal regulated kinase) signaling pathway in the absence of exogenous soluble factors. The use of a micropatterned platform to coerce human mesenchymal stem cells to adopt an elongated morphology bypasses the need to use pharmacological factors to repress FAK–ERK signaling activity to bring about substantial myogenesis.
Fabrication and properties of nanoporous GaN films (2004)

Nanopore arrays with pore diameters of approximately 75nm were fabricated in GaN films by inductively coupled plasma etching using anodic aluminum oxide (AAO) films as etch masks. Nanoporous AAO films were formed on the GaN surface by evaporating an Al film onto a GaN epilayer and subsequently anodizing the aluminum. To minimize plasma-induced damage, the template was exposed to CF4-based plasma conditions. Scanning electron microscopy analysis shows that the diameter and the periodicity of the nanopores in the GaN were directly transferred from the original anodic alumina template. The pore diameter in the AAO film can be easily controlled by tuning the anodization conditions. Atomic force microscopy, photoluminescence, and micro-Raman techniques were employed to assess the etched GaN nanopore surface. This cost-effective, nonlithographic method to produce nano-patterned GaN templates is expected to be useful for growth and fabrication of nitride-based nanostructures and photonic band gap materials.
Effects of Leukocytic Pyrogen (Interleukin-1) on Local Cerebral Glucose Utilization in Rats with and without Premedication with Indomethacin or Dexamethasone (1988)

Changes in body temperature were recorded in freely moving rats given phosphate-buffered saline or leukocytic pyrogen (interleukin-1) while the animals were in an infant incubator maintained at 25.5 +/- 0.5 degrees C. The leukocytic pyrogen increased body temperature by at least 1 degree C within 1 h. This rise in temperature was prevented by premedication with indomethacin (10 mg/kg) but not dexamethasone (0.5 mg/kg) given 15 min before the leukocytic pyrogen. Local rates of glucose utilization were measured in 47 regions of the central nervous system. In none of the regions previously reported to have an increased rate of glucose utilization associated with an ambient temperature of 32.5 degrees C (McCulloch et al., 1982b) was an increase found in the present experiments. It was concluded that the intensity of the changes in local cerebral glucose utilization in response to the fever caused by the leukocytic pyrogen was insufficient to be measured. Neither indomethacin nor dexamethasone caused remarkable changes in rates of local glucose utilization.
Improved performance and cost reduction of RO seawater systems using pretreatment (1999)

Reverse osmosis seawater systems that operate on a surface feed-water, originating from an open intake source, require an extensive pretreatment process in order to control membrane fouling. Considerations of long-term performance stability lead to a design concept of operation at a low permeate flux rate and low permeate recovery. In recent years, the nominal performance of composite seawater membrane elements has improved significantly, and new effective water microfiltration technologies have been introduced commercially. These developments can be used to improve the quality of surface seawater feed to the level comparable with, or better than, the quality of water derived from well sources. They also allow more advanced reverse osmosis systems to be designed, which should result in increased reliability and lower water costs, as this article shows.
Ohmic contact technology in III-V nitrides using polarization effects in cap layers (2003)

A novel technology for low-resistance ohmic contacts to III-V nitrides is presented. The contacts employ polarization-induced electric fields in strained cap layers grown on lattice-mismatched III-V nitride buffer layers. With appropriate choice of the cap layer, the electric field in the cap layer reduces the thickness of the tunnel barrier at the metal contact/semiconductor interface. Design rules for polarization-enhanced contacts are presented giving guidance for composition and thickness of the cap layer for different III-V nitride buffer layers. Experimental results for ohmic contacts with p-type InGaN and GaN cap layers are markedly different from samples without a polarized cap layer thus confirming the effectiveness of polarization-enhanced ohmic contacts.