gebhart/patrepeval huggingface dataset:
Common Structural and Epigenetic Changes in the Genome of Castration-Resistant Prostate Cancer (2011)

Progression of primary prostate cancer to castration-resistant prostate cancer (CRPC) is associated with numerous genetic and epigenetic alterations that are thought to promote survival at metastatic sites. In this study, we investigated gene copy number and CpG methylation status in CRPC to gain insight into specific pathophysiologic pathways that are active in this advanced form of prostate cancer. Our analysis defined and validated 495 genes exhibiting significant differences in CRPC in gene copy number, including gains in androgen receptor (AR) and losses of PTEN and retinoblastoma 1 (RB1). Significant copy number differences existed between tumors with or without AR gene amplification, including a common loss of AR repressors in AR-unamplified tumors. Simultaneous gene methylation and allelic deletion occurred frequently in RB1 and HSD17B2, the latter of which is involved in testosterone metabolism. Lastly, genomic DNA from most CRPC was hypermethylated compared with benign prostate tissue. Our findings establish a comprehensive methylation signature that couples epigenomic and structural analyses, thereby offering insights into the genomic alterations in CRPC that are associated with a circumvention of hormonal therapy. Genes identified in this integrated genomic study point to new drug targets in CRPC, an incurable disease state which remains the chief therapeutic challenge.
Ethanol and the Liver (2002)

Distilling the available knowledge on ethanol-induced liver damage and directly complementing the available bio-medical literature, Ethanol and the Liver covers pathogenic and clinical aspects of alcoholic liver disease. Providing broader coverage of the subject than any available monograph, the editors and their panel of experts relate basic scien
CLIP: Carbon Dioxide testing suitable for Low power microelectronics and IOT interfaces using Room temperature Ionic Liquid Platform (2020)

Health and safety considerations of room occupants in enclosed spaces is crucial for building management which entails control and stringent monitoring of CO<sub>2</sub> levels to maintain acceptable air quality standards and improve energy efficiency. Smart building management systems equipped with portable, low-power, non-invasive CO<sub>2</sub> sensing techniques can predict room occupancy detection based on CO<sub>2</sub> levels exhaled by humans. In this work, we have demonstrated the development and proof-of-feasibility working of an electrochemical RTIL- based sensor prototype for CO<sub>2</sub> detection in exhaled human breath. The portability, small form factor, embedded RTIL sensing element, integrability with low-power microelectronic and IOT interfaces makes this CO<sub>2</sub> sensor prototype a potential application for passive room occupancy monitoring. This prototype exhibits a wide dynamic range of 400-8000 ppm, a short response time of ~10 secs, and a reset time of ~6 secs in comparison to commercial standards. The calibration response of the prototype exhibits an R<sup>2</sup> of 0.956. With RTIL as the sensing element, we have achieved a sensitivity of 29 pF/ppm towards CO<sub>2</sub> at ambient environmental conditions and a three times greater selectivity towards CO<sub>2</sub> in the presence of N<sub>2</sub> and O<sub>2</sub>. CO<sub>2</sub> detection is accomplished by quantifying the capacitance modulations arising within the electrical double layer from the RTIL- CO<sub>2</sub> interactions through AC- based electrochemical impedance spectroscopy and DC- based chronoamperometry.
Successful Surgery of Malignant Fibrous Histiocytoma in the Lung with Gross Extension into the Right Main Pulmonary Artery (1993)

We report on successful surgical treatment of a 49-year-old female suffering from malignant fibrous histiocytoma which arose from the lower lobe of the right lung with gross extension into the right main pulmonary artery, mimicking pulmonary thromboembolism. With the aid of a percutaneous cardiopulmonary support system, right pneumonectomy with resection of the right main pulmonary artery and reconstruction of the pulmonary artery was performed. Surgical management and the unique clinicopathological features of this case are discussed.
A Well-Controlled BioID Design for Endogenous Bait Proteins (2018)

The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate the overexpression of bait proteins. Control cell lines are typically nonengineered cells or engineered clones, implying a considerable risk for artifacts because of clonal variation. Genome engineering can also transform BioID, a proximity labeling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bicistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A autocleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over the classical ectopic expression of p53-BirA*, and we provide a first well-controlled view of the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.
Kinetics of phosphorothioate oligonucleotide metabolism in biological fluids (1997)

The in vitro stability and metabolism of GEM[91, a 25mer phosphorothioate antisense oligonucleotide complementary to the gag mRNA region of HIV-1, was investigated using capillary electrophoresis (CE). The in vitro degradation of the parent compound at 37 degrees C was followed over the course of 120 h in human plasma. A CE method using laser-induced fluorescence detection was able to detect 5'-end intact metabolites including the parent compound extracted from biological fluids. Because the primary metabolic pathway is believed to be via 3'-exonuclease activity, the results of this study were compared with the stability of the compound in a solution containing 3'-exonuclease. The numerical solution of sequential first-order reactions was used to obtain kinetic parameters. Exonuclease digestion of the parent compound, as measured using an automated CE-UV instrument, yielded striking similarities between the two in vitro systems as well as between in vitro and in vivo systems.
Regioselective Galactofuranosylation for the Synthesis of Disaccharide Patterns Found in Pathogenic Microorganisms (2017)

Koenigs-Knorr glycosylation of acceptors with more than one free hydroxyl group by 2,3,5,6-tetrabenzoyl galactofuranosyl bromide was performed using diphenylborinic acid 2-aminoethyl ester (DPBA) as inducer of regioselectivity. High regioselectivity for the glycosylation on the equatorial hydroxyl group of the acceptor was obtained thanks to the transient formation of a borinate adduct of the corresponding 1,2-cis diol. Nevertheless formation of orthoester byproducts hampered the efficiency of the method. Interestingly electron-withdrawing groups on O-6 or on C-1 of the acceptor displaced the reaction in favor of the desired galactofuranosyl containing disaccharide. The best yield was obtained for the furanosylation of p-nitrophenyl 6-O-acetyl mannopyranoside. Precursors of other disaccharides, found in the glycocalix of some pathogens, were synthesized according to the same protocol with yields ranging from 45 to 86%. This is a good alternative for the synthesis of biologically relevant glycoconjugates.
Appendix A - Some Subtleties in Speckle Simulation With the 4f Imaging System (2022)

As pointed out in Section 1.3, there are some subtleties associated with the generation of simulated speckle using the 4f imaging system that arise from the finite size of the arrays used in the simulation. The phenomenon involves a complicated relationship between the size of the arrays used and the diameter of the focal-plane stop. It is possible to choose these parameters in such a way that the contrast of the speckle (i.e., the standard deviation of intensity normalized by the mean intensity) never achieves its ideal value of unity.
Communist China Today. Vol. 2. Chronological and Documentary Supplement (1959)

Communist China Today. Vol. 2. Chronological and Documentary Supplement Get access Communist China Today. Vol. 2. Chronological and Documentary Supplement. By Peter S. H. Tang. New York, Praeger; London, Atlantic Book distributed by Stevens, 1958. vi+137 pp. Map endpapers. 30s. Roderick MacFarquhar Roderick MacFarquhar Search for other works by this author on: Oxford Academic Google Scholar International Affairs, Volume 35, Issue 1, January 1959, Pages 130–131, https://doi.org/10.2307/2607120 Published: 01 January 1959
ChemInform Abstract: Synthesis, Structure, and Pharmacological Evaluation of the Stereoisomers of Furnidipine. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
N-terminal pro-B-type natriuretic peptide (NT-proBNP) in HIV-1 infected individuals on HAART. (2007)

HIV infected individuals had higher NT-proBNP levels than age matched blood donors possibly as a result of a higher prevalence of general cardiovascular risk factors and HIV associated risk factors, the finding is consistent with an increased incidence of cardiovascular events described in HIV infected individuals. Further studies on the relationship to cardiovascular outcome are warranted.
High pretransplant HBV level predicts HBV reactivation after kidney transplantation in HBV infected recipients (2014)

Effective viral suppression with antiviral agents in HBsAg-positive renal transplant recipients improves patient outcome and allograft survival. Antiviral therapy may be especially beneficial in patients with high HBV DNA levels prior to transplantation.
Robustness of the ferret model for influenza risk assessment studies: a cross-laboratory exercise (2022)

Abstract Ferrets represent the preferred animal model for assessing the transmission potential of newly emerged zoonotic influenza viruses. However, heterogeneity among established experimental protocols and facilities across different laboratories may lead to variable results, complicating interpretation of transmission experimental data. Between 2018-2020, a global exercise was conducted by 11 participating laboratories to assess the range of variation in ferret transmission experiments using two common stock H1N1 influenza viruses that possess different transmission characteristics in ferrets. Inoculation route, dose, and volume were standardized, and all participating laboratories followed the same experimental conditions for respiratory droplet transmission, including a strict 1:1 donor:contact ratio. Additional host and environmental parameters likely to affect influenza transmission kinetics were monitored throughout. Overall transmission outcomes for both viruses across 11 laboratories were concordant, suggesting the robustness of the ferret model for zoonotic influenza risk assessment. To attain high confidence in identifying zoonotic influenza viruses with moderate-to-high or low transmissibility, our analyses support that as few as three but as many as five laboratories, respectively, would need to independently perform viral transmission experiments with concordant results. This exercise facilitates the development of a more homogenous protocol for ferret transmission experiments that are employed for the purposes of risk assessment.
Adiponectin in mice with altered GH action: links to insulin sensitivity and longevity? (2012)

Adiponectin is positively correlated with longevity and negatively correlated with many obesity-related diseases. While there are several circulating forms of adiponectin, the high-molecular-weight (HMW) version has been suggested to have the predominant bioactivity. Adiponectin gene expression and cognate serum protein levels are of particular interest in mice with altered GH signaling as these mice exhibit extremes in obesity that are positively associated with insulin sensitivity and lifespan as opposed to the typical negative association of these factors. While a few studies have reported total adiponectin levels in young adult mice with altered GH signaling, much remains unresolved, including changes in adiponectin levels with advancing age, proportion of total adiponectin in the HMW form, adipose depot of origin, and differential effects of GH vs IGF1. Therefore, the purpose of this study was to address these issues using assorted mouse lines with altered GH signaling. Our results show that adiponectin is generally negatively associated with GH activity, regardless of age. Further, the amount of HMW adiponectin is consistently linked with the level of total adiponectin and not necessarily with previously reported lifespan or insulin sensitivity of these mice. Interestingly, circulating adiponectin levels correlated strongly with inguinal fat mass, implying that the effects of GH on adiponectin are depot specific. Interestingly, rbGH, but not IGF1, decreased circulating total and HMW adiponectin levels. Taken together, these results fill important gaps in the literature related to GH and adiponectin and question the frequently reported associations of total and HMW adiponectin with insulin sensitivity and longevity.
Frontispiz: Amine‐Directed Formation of B−N Bonds for BN‐Fused Polycyclic Aromatic Multiple Resonance Emitters with Narrowband Emission (2022)

Organische Halbleiter. Eine Amin-dirigierte B-N-Bindungsbildung für die Synthese von BN-fusionierten polycyclischen aromatischen Mehrfachresonanzemittern wird in der Zuschrift (e202207293) von Dongdong Zhang, Lian Duan et al. vorgestellt.
ChemInform Abstract: A Cyclic Sulfate Route to Methylenecyclopropanes. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An Immunoassay Platform based on CMOS Hall Sensors (2002)

We describe an immunoassay utilizing standard CMOS technology. An array of Hall sensors is used to detect the magnetic beads that serve as the assay signal. Electrical and magnetic modulation is employed to improve the sensitivity of the sensors. The devices receive two post-processing steps to improve sensitivity and biocompatibility. We have fabricated prototype devices using a 0.25-m BiCMOS process, and have successfully detected anti-Hu IgG antibody at a concentration of 200pM.
Spreading code detection and blind interference cancellation for DS/CDMA downlink (2005)

We propose a new blind interference scheme algorithm suitable for the direct-sequence code-division multiple access (DS/CDMA) downlink. The interferer codes are unknown but the family to which they belong is supposed to be known. The proposed technique is blind in the sense that only the desired user's spreading code is assumed to be known a priori. The remaining parameters required for the interference cancellation such as spreading codes and energies of interfering users are estimated using subspace decomposition and projection on the family of codes. Fast and efficient implementations are discussed. Therefore, unlike standard interference cancellers which can be used only in the uplink, the proposed method can be implemented at the mobile terminal.
Mass spectrometric characterization of urinary metabolites of the selective androgen receptor modulator S‐22 to identify potential targets for routine doping controls (2011)

Drugs that promote anabolic processes with limited undesirable effects are of considerable therapeutic interest; some notable examples include those for the treatment of cancer cachexia and muscle-wasting diseases. Anabolic properties are not only therapeutically beneficial to critically ill and debilitated patients, but are also desirable to athletes seeking artificial enhancements in endurance, strength and accelerated recovery. The use of anabolic agents in the clinical setting is being reconsidered with the emergence of a new class of drugs referred to as SARMs (selective androgen receptor modulators). SARMs have the potential to complement or even replace anabolic androgenic steroidal use with the benefit of a reduction of the undesirable side effects associated with steroid administration alone. Arylpropionamide-based SARMs such as andarine (S-4) and S-22 have shown promising therapeutic properties and have attracted the interest of elite and amateur athletes despite the absence of clinical approval, and evidence for trafficking and misuse in sport has been obtained by doping control authorities. In this communication, the elucidation of urinary metabolites of the SARM drug candidate S-22 is compared with earlier in vitro metabolism studies. Following oral administration of illicit S-22, urine samples were collected after 62 and 135 h and analyzed for the active drug and its major metabolic products. Liquid chromatography interfaced with high-resolution/high-accuracy (tandem) mass spectrometry was used to identify and/or confirm the predicted target analytes for sports drug testing purposes. S-22 was detected in both specimens accompanied by its glucuronic acid conjugate. This was the B-ring hydroxylated derivative of S-22 plus the corresponding glucuronide (with the phase-II metabolites being the more abundant analytes). In addition, the samples collected 62 h post-administration also contained the phase-I metabolite hydroxylated at the methyl residue (C-20) and the B-ring depleted degradation product ('dephenylated' S-22) together with the corresponding carboxy analog that was previously reported for canine metabolism. The obtained data supports future efforts to effectively screen for and confirm the misuse of the non-approved S-22 drug candidate in doping controls.
A 60GHz CMOS class C amplifier intended for use in Doherty architecture (2012)

A 60GHz CMOS class C power amplifier was designed and fabricated for use in Doherty architecture as the peaking amplifier. It was designed to have high output impedance at power back-off and high output power at peak power. The measurements showed that there is a frequency shift compared to the simulations due to model inaccuracies, but the high output impedance was achieved along with the high output power. Simulation results show that by using the designed power amplifier in the Doherty architecture, a PAE of 12% can be achieved at 6dB output power back-off.
Robustness of Local Binary Patterns in Brain MR Image Analysis (2007)

The aging population in developed countries has shifted considerable research attention to diseases related to age. Because age is one of the highest risk factors for neurodegenerative diseases, the need for automated brain image analysis has significantly increased. Magnetic Resonance Imaging (MRI) is a commonly used modality to image brain. MRI provides high tissue contrast; hence, the existing brain image analysis methods have often preferred the intensity information to others, such as texture. Recently, an easy-to-compute texture descriptor, Local Binary Pattern (LBP), has shown promise in various applications outside the medical field. In this paper, after extensive experiments, we show that rotation-invariant LBP is invariant to some common MRI artifacts that makes it possible to use it in various high-level brain MR image analysis applications.
Technoeconomic and life-cycle analysis of single-step catalytic conversion of wet ethanol into fungible fuel blendstocks (2019)

Technoeconomic and life-cycle analyses are presented for catalytic conversion of ethanol to fungible hydrocarbon fuel blendstocks, informed by advances in catalyst and process development. Whereas prior work toward this end focused on 3-step processes featuring dehydration, oligomerization, and hydrogenation, the consolidated alcohol dehydration and oligomerization (CADO) approach described here results in 1-step conversion of wet ethanol vapor (40 wt% in water) to hydrocarbons and water over a metal-modified zeolite catalyst. A development project increased liquid hydrocarbon yields from 36% of theoretical to >80%, reduced catalyst cost by an order of magnitude, scaled up the process by 300-fold, and reduced projected costs of ethanol conversion 12-fold. Current CADO products conform most closely to gasoline blendstocks, but can be blended with jet fuel at low levels today, and could potentially be blended at higher levels in the future. Operating plus annualized capital costs for conversion of wet ethanol to fungible blendstocks are estimated at $2.00/GJ for CADO today and $1.44/GJ in the future, similar to the unit energy cost of producing anhydrous ethanol from wet ethanol ($1.46/GJ). Including the cost of ethanol from either corn or future cellulosic biomass but not production incentives, projected minimum selling prices for fungible blendstocks produced via CADO are competitive with conventional jet fuel when oil is $100 per barrel but not at $60 per barrel. However, with existing production incentives, the projected minimum blendstock selling price is competitive with oil at $60 per barrel. Life-cycle greenhouse gas emission reductions for CADO-derived hydrocarbon blendstocks closely follow those for the ethanol feedstock.
5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox (2018)

Moxetumomab pasudotox (Moxe) is a chimeric protein composed of an anti-CD22 Fv fused to a portion of <i>Pseudomonas</i> exotoxin A and kills CD22-expressing leukemia cells. It is very active in hairy-cell leukemia, but many children with relapsed/refractory acute lymphoblastic leukemia (ALL) either respond transiently or are initially resistant. Resistance to Moxe in cultured cells is due to low expression of diphthamide genes (DPH), but only two of six ALL blast samples from resistant patients had low DPH expression. To develop a more clinically relevant model of resistance, we treated NSG mice bearing KOPN-8 or Reh cells with Moxe. More than 99.9% of the cancer cells were killed by Moxe, but relapse occurred from discrete bone marrow sites. The resistant cells would no longer grow in cell culture and showed major chromosomal changes and changes in phenotype with greatly decreased CD22. RNA deep sequencing of resistant KOPN-8 blasts revealed global changes in gene expression, indicating dedifferentiation toward less-mature B cell precursors, and showed an up-regulation of myeloid genes. When Moxe was combined with 5-azacytidine, resistance was prevented and survival increased to over 5 months in the KOPN-8 model and greatly improved in the Reh model. We conclude that Moxe resistance in mice is due to a new mechanism that could not be observed using cultured cells and is prevented by treatment with 5-azacytidine.
Out‐of‐hospital health care costs of childhood food allergy in Australia: A population‐based longitudinal study (2022)

Childhood food allergy causes considerable Medicare costs for out-of-hospital services in the first four years after birth in Australia. These findings can help anticipate the financial impact on the health care system associated with childhood food allergy, act as a useful costing resource for future evaluations, and inform management of childhood food allergy internationally.