gebhart/patrepeval huggingface dataset:
The incidence, risk factors, and outcome of transfusion-related acute lung injury in a cohort of cardiac surgery patients: a prospective nested case-control study (2011)

Transfusion-related acute lung injury (TRALI) is the leading cause of transfusion-related morbidity and mortality. Both antibodies and bioactive lipids that have accumulated during storage of blood have been implicated in TRALI pathogenesis. In a single-center, nested, case-control study, patients were prospectively observed for onset of TRALI according to the consensus definition. Of 668 patients, 16 patients (2.4%) developed TRALI. Patient-related risk factors for onset of TRALI were age and time on the cardiopulmonary bypass. Transfusion-related risk factors were total amount of blood products (odds ratio [OR] = 1.2; 95% confidence interval [CI], 1.03-1.44), number of red blood cells stored more than 14 days (OR = 1.6; 95% CI, 1.04-2.37), total amount of plasma (OR = 1.2; 95% CI, 1.03-1.44), presence of antibodies in donor plasma (OR = 8.8; 95% CI, 1.8-44), and total amount of transfused bioactive lipids (OR = 1.0; 95% CI, 1.00-1.07). When adjusted for patient risk factors, only the presence of antibodies in the associated blood products remained a risk factor for TRALI (OR = 14.2; 95% CI, 1.5-132). In-hospital mortality of TRALI was 13% compared with 0% and 3% in transfused and nontransfused patients, respectively (P < .05). In conclusion, the incidence of TRALI is high in cardiac surgery patients and associated with adverse outcome. Our results suggest that cardiac surgery patients may benefit from exclusion of blood products containing HLA/HNA antibodies.
Synthesis and Functional Analyses of Nuclear Clusterin, a Cell Death Protein (2003)

Nuclear clusterin (nCLU) is an ionizing radiation (IR)-inducible protein that binds Ku70, and triggers apoptosis when overexpressed in MCF-7 cells. We demonstrate that endogenous nCLU synthesis is a product of alternative splicing. Reverse transcriptase-PCR analyses revealed that exon II, containing the first AUG and encoding the endoplasmic reticulum-targeting peptide, was omitted. Exons I and III are spliced together placing a downstream AUG in exon III as the first available translation start site. This shorter mRNA produces the 49-kDa precursor nCLU protein. Ku70 binding activity was localized to the C-terminal coiled-coil domain of nCLU. Leucine residues 357, 358, and 361 of nCLU were necessary for Ku70-nCLU interaction. The N- and C-terminal coiled-coil domains of nCLU interacted with each other, suggesting that the protein could dimerize or fold. Mutation analyses indicate that the C-terminal NLS was functional in nCLU with the same contribution from N-terminal NLS. The C-terminal coiled-coil domain of nCLU was the minimal region required for Ku binding and apoptosis. MCF-7 cells show nuclear as well as cytoplasmic expression of GFP-nCLU in apoptotic cells. Cytosolic aggregation of GFP-nCLU was found in viable cells. These results indicate that an inactive precursor of nCLU exists in the cytoplasm of non-irradiated MCF-7 cells, translocates into the nucleus following IR, and induces apoptosis.
Selective interleukin-1 receptor–associated kinase 4 inhibitors for the treatment of autoimmune disorders and lymphoid malignancy (2015)

Pathological activation of the Toll-like receptor signaling adaptor protein MYD88 underlies many autoimmune and inflammatory disease states. In the activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL), the oncogenic MYD88 L265P mutation occurs in 29% of cases, making it the most prevalent activating mutation in this malignancy. IRAK4 kinase accounts for almost all of the biological functions of MYD88, highlighting IRAK4 as a therapeutic target for diseases driven by aberrant MYD88 signaling. Using innovative structure-based drug design methodologies, we report the development of highly selective and bioavailable small molecule IRAK4 inhibitors, ND-2158 and ND-2110. These small molecules suppressed LPS-induced TNF production, alleviated collagen-induced arthritis, and blocked gout formation in mouse models. IRAK4 inhibition promoted killing of ABC DLBCL lines harboring MYD88 L265P, by down-modulating survival signals, including NF-κB and autocrine IL-6/IL-10 engagement of the JAK-STAT3 pathway. In ABC DLBCL xenograft models, IRAK4 inhibition suppressed tumor growth as a single agent, and in combination with the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib or the Bcl-2 inhibitor ABT-199. Our findings support pharmacological inhibition of IRAK4 as a therapeutic strategy in autoimmune disorders, in a genetically defined population of ABC DLBCL, and possibly other malignancies dependent on aberrant MYD88 signaling.
Identification of a gene encoding an acyl CoA:diacylglycerol acyltransferase, a key enzyme in triacylglycerol synthesis (1998)

Triacylglycerols are quantitatively the most important storage form of energy for eukaryotic cells. Acyl CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the terminal and only committed step in triacylglycerol synthesis, by using diacylglycerol and fatty acyl CoA as substrates. DGAT plays a fundamental role in the metabolism of cellular diacylglycerol and is important in higher eukaryotes for physiologic processes involving triacylglycerol metabolism such as intestinal fat absorption, lipoprotein assembly, adipose tissue formation, and lactation. DGAT is an integral membrane protein that has never been purified to homogeneity, nor has its gene been cloned. We identified an expressed sequence tag clone that shared regions of similarity with acyl CoA:cholesterol acyltransferase, an enzyme that also uses fatty acyl CoA as a substrate. Expression of a mouse cDNA for this expressed sequence tag in insect cells resulted in high levels of DGAT activity in cell membranes. No other acyltransferase activity was detected when a variety of substrates, including cholesterol, were used as acyl acceptors. The gene was expressed in all tissues examined; during differentiation of NIH 3T3-L1 cells into adipocytes, its expression increased markedly in parallel with increases in DGAT activity. The identification of this cDNA encoding a DGAT will greatly facilitate studies of cellular glycerolipid metabolism and its regulation.
19.4 A 2.7-to-3.7GHz rapid interferer detector exploiting compressed sampling with a quadrature analog-to-information converter (2015)

Mobile data traffic (driven by video over wireless, Internet of Things and machine-to-machine communications) is predicted to grow by several orders of magnitude over the coming decades, leading to severe spectrum deficits (500MHz to 1GHz in the near to long term). In 2012 the US President's Council of Advisors on Science and Technology (PCAST) recommended sharing government spectrum from 2.7GHz to 3.7GHz for public use while advocating that future systems deliver significantly improved spectrum efficiency. Cognitive radio systems with multi-tiered shared spectrum access (MTSSA) are expected to deliver such superior efficiency over existing scheduled-access systems; they have 3 or more device tiers with different access privileges. Lower tiered `smart' devices opportunistically use the underutilized spectrum and need spectrum sensing for incumbent detection and interférer avoidance. Incumbent detection will rely on database lookup or narrowband high-sensitivity sensing. Integrated interférer detectors, on the other hand, need to be fast, wideband and energy efficient while only requiring moderate sensitivity. During designated slot boundaries (10s of us), they quickly detect the presence of a few (3 or so) large interferers over e.g., a 1GHz span (2.7 to 3.7GHz) with a 20MHz RBW (i.e. 50 bins) so that the carrier-aggregating receiver can be reconfigured on a frame (10s of ms) or even slot (100s of us) basis.
Mixed integer programming for multi-vehicle path planning (2001)

This paper presents a new approach to fuel-optimal path planning of multiple vehicles using a combination of linear and integer programming. The basic problem formulation is to have the vehicles move from an initial dynamic state to a final state without colliding with each other, while at the same time avoiding other stationary and moving obstacles. It is shown that this problem can be rewritten as a linear program with mixed integer/linear constraints that account for the collision avoidance. A key benefit of this approach is that the path optimization can be readily solved using the CPLEX optimization software with an AMPL/Matlab interface. An example is worked out to show that the framework of mixed integer/linear programming is well suited for path planning and collision avoidance problems. Implementation issues are also considered. In particular, we compare receding horizon strategies with fixed arrival time approaches.
Liquid-liquid and vapour-liquid behaviour of oleyl alcohol applied to extractive fermentation processing (1993)

Investigations into the product recovery step of the extractive ethanol fermentation through partition experiments for ethanol-water-Adolr̀ 85 NF ternary systems were undertaken. Experimental liquid-liquid equilibrium data for this ternary system were compared with numerical predictions based on the UNIFAC method. The influence of salts on distribution coefficients for ethanol extraction was also examined. An improvement in extraction characteristics was observed for ternary systems with salts. Flash vaporisation was used to subsequently examine the effect of liquid-liquid ternary compositions on vapour-liquid partitioning. The UNIFAC model was found to be very useful for semi-quantitative analysis of such liquid extraction systems. On a effectué des recherches sur ľétape de récupération des produits lors de la fermentation extractive ďéthanol par des expériences de séparation pour des systèmes ternaires éthanol-eau-Adolr̀ 85 NF. Les données ďéquilibre liquide-liquide expérimentales pour ce système ternaire ont été comparées aux prédictions numériques basées sur la méthode UNIFAC. On a également examiné ľinfluence des sels sur les coefficients de distribution pour ľextraction de ľéthanol. Une amélioration des caractéristiques ďextraction a été observée pour les systèmes ternaires en présence de sels. Par la suite, on a eu recours à la vaporisation éclair pour examiner ľeffet des compositions ternaires liquide-Iiquide sur la séparation liquide-vapeur. Le modèle UNIFAC 'est révélé très utile pour ľanalyse semi-quantitative de tels systèmes ďextraction liquide.
CD34+CD33- cells influence days to engraftment and transfusion requirements in autologous blood stem-cell recipients. (1998)

These findings show that CD34+33- cells are readily collected in most cancer patients and significantly influence engraftment kinetics and transfusion requirements in autologous blood stem-cell recipients. CD34+33- cell quantity of the blood stem-cell graft appears to be a more reliable predictor of hematopoietic recovery rates than total CD34+ cell quantity in this setting.
Antibody signature induced by SARS-CoV-2 spike protein immunogens in rabbits (2020)

Multiple vaccine candidates against SARS-CoV-2 based on viral spike protein are under development. However, there is limited information on the quality of antibody responses generated with these vaccine modalities. To better understand antibody responses induced by spike protein-based vaccines, we performed a qualitative study by immunizing rabbits with various SARS-CoV-2 spike protein antigens: S ectodomain (S1+S2; amino acids 16 to 1213), which lacks the cytoplasmic and transmembrane domains (CT-TM), the S1 domain (amino acids 16 to 685), the receptor binding domain (RBD) (amino acids 319 to 541), and the S2 domain (amino acids 686 to 1213, lacking the RBD, as control). Resulting antibody quality and function were analyzed by enzyme-linked immunosorbent assay (ELISA), RBD competition assay, surface plasmon resonance (SPR) against different spike proteins in native conformation, and neutralization assays. All three antigens (S1+S2 ectodomain, S1 domain, and RBD), but not S2, generated strong neutralizing antibodies against SARS-CoV-2. Vaccination-induced antibody repertoire was analyzed by SARS-CoV-2 spike genome fragment phage display libraries (SARS-CoV-2 GFPDL), which identified immunodominant epitopes in the S1, S1-RBD, and S2 domains. Furthermore, these analyses demonstrated that the RBD immunogen elicited a higher antibody titer with five-fold higher affinity antibodies to native spike antigens compared with other spike antigens, and antibody affinity correlated strongly with neutralization titers. These findings may help guide rational vaccine design and facilitate development and evaluation of effective therapeutics and vaccines against COVID-19 disease.
General method for determining anaerobic biodegradation potential (1984)

A simple, generalized method was refined and validated to test whether an organic chemical was susceptible to anaerobic degradation to CH4 + CO2. The method used digested sewage sludge diluted to 10% and incubated anaerobically in 160-ml serum bottles with 50 micrograms of C per ml of test chemical. Biodegradation was determined by the net increase in gas pressure in bottles with test chemicals over the pressure in nonamended sludge bottles. Gas production was measured by gas chromatography and by a pressure transducer. The latter method is recommended because of its speed, accuracy, and low cost. Sewage sludge from municipal digesters with 15- to 30-day retention times was found to be suitable. The sludge could be stored anaerobically at 4 degrees C for up to 4 weeks with satisfactory test results. p-Cresol, phthalic acid, and ethanol are suggested as reference chemicals to confirm sludge activity and method reliability. A revised anaerobic salts medium was developed which minimizes problems of a biological gas production (CO2), avoids precipitation, and meets the requirements of the anaerobic microbiota. When greater than 75% of the theoretical gas production was observed, the chemical was judged to be degradable, and when 30 to 75% of the expected gas was produced, it was termed partially degradable. This method has been tested on more than 100 chemicals of various physical properties and found to reproducibly determine anaerobic biodegradation potential. Of the chemicals tested, 46 were found to be anaerobically degraded. Sludges from nine different municipal treatment plants were surveyed for their ability to degrade nine chemicals which differed in susceptibility to degradation.(ABSTRACT TRUNCATED AT 250 WORDS)
Scanning microwave-induced thermoacoustic tomography: Signal, resolution, and contrast (2001)

Scanning thermoacoustic tomography was explored in the microwave region of the electromagnetic spectrum. Short microwave pulses were used to induce acoustic waves by thermoelastic expansion in biological tissues. Cross sections of tissue samples were imaged by a linear scan of the samples while a focused ultrasonic transducer detected the time-resolved thermoacoustic signals. Based on the microwave-absorption properties of normal and cancerous breast tissues, the piezoelectric signals in response to the thermoacoustic contrast were investigated over a wide range of electromagnetic frequencies and depths of tumor locations. The axial resolution is related to the temporal profile of the microwave pulses and to the impulse response of the ultrasonic transducer. The lateral resolution is related to the numerical aperture of the ultrasonic transducer as well as to the frequency spectra of the piezoelectric signals in the time window corresponding to the axial resolution. Gain compensation, counteracting the microwave attenuation, was applied to enhance the image contrast.
Adenosine Deaminase Acting on RNA 1 (ADAR1) Suppresses the Induction of Interferon by Measles Virus (2012)

ADAR1, the interferon (IFN)-inducible adenosine deaminase acting on RNA, catalyzes the C-6 deamination of adenosine (A) to produce inosine (I) in RNA substrates with a double-stranded character. Because double-stranded RNA is a known inducer of IFN, we tested the role of ADAR1 in IFN induction following virus infection. HeLa cells made stably deficient in ADAR1 (ADAR1(kd)) were compared to vector control (CON(kd)) and protein kinase PKR-deficient (PKR(kd)) cells for IFN-β induction following infection with either parental (wild-type [WT]) recombinant Moraten vaccine strain measles virus (MV) or isogenic knockout mutants deficient for either V (V(ko)) or C (C(ko)) protein expression. We observed potent IFN-β transcript induction in ADAR1(kd) cells by all three viruses; in contrast, in ADAR1-sufficient CON(kd) cells, only the C(ko) mutant virus was an effective inducer and the IFN-β RNA induction was amplified by PKR. The enhanced IFN-β transcript-inducing capacity of the WT and V(ko) viruses seen in ADAR1-deficient cells correlated with the enhanced activation of PKR, IFN regulatory factor IRF3, and activator of transcription ATF2, reaching levels similar to those seen in C(ko) virus-infected cells. However, the level of IFN-β protein produced was not proportional to the level of IFN-β RNA but rather correlated inversely with the level of activated PKR. These results suggest that ADAR1 functions as an important suppressor of MV-mediated responses, including the activation of PKR and IRF3 and the induction of IFN-β RNA. Our findings further implicate a balanced interplay between PKR and ADAR1 in modulating IFN-β protein production following virus infection.
Elementary analysis of chemical electric field effects in biological macromolecules. 2: Kinetic aspects of electro-optic and conductometric relaxations (1986)

Electric field effects in macromolecular organizations such as proteins, nucleic acids, and membranes frequently involve both chemical-conformational changes and physical-orientational displacements of molecular subgroups. Electro-optic techniques in conjunction with relaxation kinetics in high electric fields provide a tool for the investigation of the complex processes encountered in bioelectric phenomena on the level of macromolecules, membrane fragments, and other cellular units. Whereas part 1 covers the thermodynamics of electric field effects, this part deals with practical and theoretical aspects of kinetics and mechanisms in aqueous solutions of macromolecules and membranes.
Synthesis and activity of novel nitropyrazines for use as hypoxic cell radiosensitizers (1984)

A series of eight novel nitropyrazines has been prepared by oxidation of sulfoximine intermediates. The partition coefficient, one-electron reduction potential, sensitizer enhancement ratio, and chronic and acute aerobic cytotoxicity have been measured for each. Two representatives of this series were tested in the Ames test and were not found to be mutagenic.
Tree Indexing on Flash Disks (2009)

Large flash disks have become an attractive alternative to magnetic hard disks, due to their high random read performance, low energy consumption and other features. However, writes, especially random writes, on the flash disk are inherently much slower than reads because of the erase-before-write mechanism. To address this asymmetry of read-write speeds in indexing on the flash disk, we propose the FD-tree, a tree index designed with the logarithmic method and fractional cascading techniques. With the logarithmic method, an FD-tree consists of the head tree - a small B+-tree on the top, and a few levels of sorted runs of increasing sizes at the bottom. This design is write-optimized for the flash disk; in particular, an index search will potentially go through more levels or visit more nodes, but random writes are limited to the head tree and are subsequently transformed into sequential ones through merging into the lower runs. With the fractional cascading technique, we store pointers, called fences, in lower level runs to speed up the search. We evaluate the FD-tree in comparison with representative B+-tree variants under a variety of workloads. Our results show that the FD-tree has a similar search performance to the standard B+-tree, and a similar update performance to the write-optimized B+-tree variant. As a result, FD-tree outperforms all these B+-tree index variants on both update- and search-intensive workloads.
Inhibition of human bone marrow fibroblast colony formation by leukemic cells (1983)

The number of bone marrow fibroblast colony formations decreases in most cases of acute leukemia before the initiation of chemotherapy. This study was undertaken to clarify the mechanism of suppression of fibroblast colony formation in leukemic patients. Titration of the number of bone marrow cells did not indicate a linear relationship between the number of bone marrow cells cultured and the number of fibroblast colony formations. The number of fibroblast colony formations recovered by removal of nonadherent leukemic cells following one day of incubation increased. The cloning efficiency of patient bone marrow still showed increases in colony formation at higher plating concentrations after the nonadherent cells were removed. When leukemic and normal bone marrow cells were cocultured, the suppressive effect of leukemic cells on normal marrow fibroblast colony formation was clearly observed. The suppressive effect disappeared at complete remission, and then reappeared at relapse. Heat-inactivated serum and bone marrow culture media from leukemic patients whose fibroblast colony formations were small in number suppressed fibroblast colony formation from normal bone marrow. From these results, it was concluded that the suppression of fibroblast colony formation in leukemic patients was through humoral factors produced by leukemic cells.
A quad-band low power single chip direct conversion CMOS transceiver with ΣΔ-modulation loop for GSM (2004)

This paper presents a fully integrated quad band GSM transceiver with a new sigma-delta modulator architecture designed in a standard 120 nm CMOS technology. The fully integrated VCO operates at 4 GHz with a frequency range that can be programmed by 10 bit. The output power of the transmitter is 8 dBm and no TX SAW filter is needed due to the low phase noise of -162 dBc/Hz at 20 MHz offset frequency. The inband phase noise of the synthesizer is only -100 dBc/Hz and an overall phase noise error of 1.6/spl deg/ rms has been measured. The receiver has constant gain of 57 dB and fits to a baseband processor providing a 14 bit ADC. The noise figure in all bands is below 3 dB typically. The chip is housed in a 48 pin VQFN package.
AKI Associated with Cardiac Surgery (2014)

Approximately 18% of patients undergoing cardiac surgery experience AKI (on the basis of modern standardized definitions of AKI), and approximately 2%-6% will require hemodialysis. The development of AKI after cardiac surgery portends poor short- and long-term prognoses, with those developing RIFLE failure or AKI Network stage III having an almost 2-fold increase in the risk of death. AKI is caused by a variety of factors, including nephrotoxins, hypoxia, mechanical trauma, inflammation, cardiopulmonary bypass, and hemodynamic instability, and it may be affected by the clinician's choice of fluids and vasoactive agents as well as the transfusion strategy used. The risk of AKI may be ameliorated by avoidance of nephrotoxins, achievement of adequate glucose control preoperatively, and use of goal-directed therapy hemodynamic strategies. Remote ischemic preconditioning is an exciting future strategy, but more work is needed before widespread implementation. Unfortunately, there are no pharmacologic agents known to reduce the risk of AKI or treat established AKI.