gebhart/patrepeval huggingface dataset:
Proposed score for survival of patients with myelodysplastic syndromes (2013)

Our newly proposed score may be a useful tool for survival prediction in MDS and helpful in patient selection for various therapies in daily practice and clinical trials.
Real-time simulator for intravascular ultrasound (IVUS) (2007)

Intravascular Ultrasound (IVUS) plays a significant role in diagnostics of atherosclerotic diseases. Simulation of imaging techniques promises a better understanding of the physical background and segmentation strategies. Most simulation approaches describe ultrasonic backscattering using wave-equation based simplifications. More complicated real-time simulation techniques are not available so far. In this paper, we present an empirical model derived from wave-equations given by the Rayleigh integration method. According to boundary conditions and weak scatterers, a hybrid approach including the Beer-Lambert law to model attenuation is introduced. Scatterers are described by a 4D vessel-system model based on elastic tubes. Sophisticated discretization and numerical simplifications in addition to a highly optimized implementation of the model yields a real-time and realistic IVUS simulation with 20 frames/s on a 3.2 GHz Pentium 4 PC.
ChemInform Abstract: KOMPLEXCHEMIE REAKTIVER ORGANISCHER VERBINDUNGEN 9. MITT. EINBAU VON METHYLEN IN MANGAN‐KOMPLEXE (1975)

Abstract Die Cyclopentadienylmangankomplexe (I) reagieren bei Raumtemperatur mit Diazomethan zu einem Gemisch der u‐Methyliden‐und n‐Äthylen‐Komplexe (III) und (IV).
Abstract PR5: Prediction of survival in diffuse large B-cell lymphoma based on the expression of two genes integrating tumor and microenvironment (2010)

Abstract Several gene expression signatures are predictive of prognosis in diffuse large B cell lymphoma (DLBCL), but the lack of practical methods for a genome scale analysis has restricted their clinical applicability. Towards construction of a molecular predictor amenable to rapid testing on routinely obtained diagnostic clinical specimens, we studied genes previously reported to be associated with survival in DLBCL, testing and validating risk scoring models with robust survival associations in the current therapeutic era. We identified LMO2 expression as a robust univariate predictor of survival and cell of origin classification of DLBCL, with independent prognostic value. We examined bivariate models combining expression of LMO2 with other genes, and identified TNFRSF9 as a tumor microenvironment gene with independent prognostic influence. A combined model integrating both LMO2 and TNFRSF9 expression was independent of “cell of origin” classification, “stromal signatures,” International Prognostic Index (IPI), and added to the predictive power of IPI. A composite model was validated in multiple independent patient cohorts using public microarray data. Using routinely obtained formalin fixed, paraffin embedded diagnostic specimens from an independent cohort, we developed a simple assay validating the clinical utility of this 2-gene model, as well as a composite model integrating the IPI. In conclusion, measurement of a single gene expressed by tumor cells and a single gene expressed by the immune microenvironment is sufficient to predict overall survival in patients with DLBCL treated with R-CHOP. A combined model serves as a robust clinical risk assessment tool. This talk is also presented as Poster A27. Citation Information: Clin Cancer Res 2010;16(14 Suppl):PR5.
Abstract 1612: Validation of CSE1L/hCAS as a potential therapeutic target in pancreatic cancer (2010)

Abstract Background: The nuclear export protein CSE1L/hCAS has recently gained attention as a putative oncogene, which is amplified in several human malignancies. The role of hCAS in pancreatic cancer is unknown. In this work, we sought to evaluate the expression of hCAS in pancreatic cancer cell lines and tumor tissue and to further explore the potential of hCAS as a therapeutic target. Methods: The nuclear and cytosolic hCAS protein expression was determined in human pancreatic cancer cell lines and tumor tissues and compared with those of immortalized normal pancreatic ductal cells and normal pancreatic tissues. The cellular effects of hCAS knockdown using small interfering RNA oligonucleotides were investigated in MiaPaCa-2 human pancreatic cancer cells with regard to proliferation (MTT assay), cell death (Trypan blue and Flow cytometry), and malignant transformation (colony formation assay). Results: hCAS protein expression increased in pancreatic cancer cell lines relative to the immortalized pancreatic ductal epithelial cell line. Immunohistochemical staining of a human pancreatic tumor tissue microarray showed that hCAS expression was higher in pancreatic tumors compared with their normal counterparts. There was increasing nuclear to cytoplasmic staining with progression from normal pancreatic duct to increasing grade of pancreatic intraductal neoplasia to invasive pancreatic cancer. Treatment with hCAS targeting small interfering RNAs effectively reduced pancreatic cell growth in tissue culture, induced apoptosis, and inhibited growth in soft agar. Conclusion: This is the first report of hCAS expression and cellular distribution in human pancreatic cancer. Our data suggest that hCAS might be an attractive target for human pancreatic cancer prevention and therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1612.
Reaction Time and Visual Memory in Connection to Hazardous Drinking Polygenic Scores in Schizophrenia, Schizoaffective Disorder and Bipolar Disorder (2021)

The purpose of this study was to explore the association of cognition with hazardous drinking Polygenic Scores (PGS) in 2649 schizophrenia, 558 schizoaffective disorder, and 1125 bipolar disorder patients in Finland. Hazardous drinking PGS was computed using the LDPred program. Participants performed two computerized tasks from the Cambridge Automated Neuropsychological Test Battery (CANTAB) on a tablet computer: the 5-choice serial reaction time task, or Reaction Time (RT) test, and the Paired Associative Learning (PAL) test. The association between hazardous drinking PGS and cognition was measured using four cognition variables. Log-linear regression was used in Reaction Time (RT) assessment, and logistic regression was used in PAL assessment. All analyses were conducted separately for males and females. After adjustment of age, age of onset, education, household pattern, and depressive symptoms, hazardous drinking PGS was not associated with reaction time or visual memory in male or female patients with schizophrenia, schizoaffective, and bipolar disorder.
The Dimer Interfaces of Protease and Extra-Protease Domains Influence the Activation of Protease and the Specificity of GagPol Cleavage (2002)

Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation.
Reducti Of Sinusoidal Contiunuous Noise in Electromagnexic Waves Using Digital Filters for Partial Discharge Measurements (2000)

This paper presents new developed noise reduction methods and results of partial discharge detection and measurements of electric power apparatus using digital signal processing techniques. We have examined noise diminution by the algorithm in laboratory based on measurements of PD signals in SF6 gas and real noise as well as interference in practical HV and EHV substations. Consequently, the techniques, enabled us to reduce sinusoidal continuous noise considerably, so that they are promising for future application in actual HV substations.
Rex in Caldicellulosiruptor bescii : Novel regulon members and its effect on the production of ethanol and overflow metabolites (2018)

Rex is a global redox-sensing transcription factor that senses and responds to the intracellular [NADH]/[NAD<sup>+</sup> ] ratio to regulate genes for central metabolism, and a variety of metabolic processes in Gram-positive bacteria. We decipher and validate four new members of the Rex regulon in Caldicellulosiruptor bescii; a gene encoding a class V aminotransferase, the HydG FeFe Hydrogenase maturation protein, an oxidoreductase, and a gene encoding a hypothetical protein. Structural genes for the NiFe and FeFe hydrogenases, pyruvate:ferredoxin oxidoreductase, as well as the rex gene itself are also members of this regulon, as has been predicted previously in different organisms. A C. bescii rex deletion strain constructed in an ethanol-producing strain made 54% more ethanol (0.16 mmol/L) than its genetic parent after 36 hr of fermentation, though only under nitrogen limited conditions. Metabolomic interrogation shows this rex-deficient ethanol-producing strain synthesizes other reduced overflow metabolism products likely in response to more reduced intracellular redox conditions and the accumulation of pyruvate. These results suggest ethanol production is strongly dependent on the native intracellular redox state in C. bescii, and highlight the combined promise of using this gene and manipulation of culture conditions to yield strains capable of producing ethanol at higher yields and final titer.
Self-Tuned Critical Anti-Hebbian Networks (2009)

It is widely recognized that balancing excitation and inhibition is important in the nervous system. When such a balance is sought by global strategies, few modes remain poised close to instability, and all other modes are strongly stable. Here we present a simple abstract model in which this balance is sought locally by units following "anti-Hebbian" evolution: all degrees of freedom achieve a close balance of excitation and inhibition and become "critical" in the dynamical sense. At long time scales, a complex "breakout" dynamics ensues in which different modes of the system oscillate between prominence and extinction; the model develops various long-tailed statistical behaviors and may become self-organized critical.
Monovalent manganese based anodes and co-solvent electrolyte for stable low-cost high-rate sodium-ion batteries (2018)

The demand of sustainable power supply requires high-performance cost-effective energy storage technologies. Here we report a high-rate long-life low-cost sodium-ion battery full-cell system by innovating both the anode and the electrolyte. The redox couple of manganese(I/II) in Prussian blue analogs enables a high-rate and stable anode. Soft X-ray absorption spectroscopy and resonant inelastic X-ray scattering provide direct evidence suggesting the existence of monovalent manganese in the charged anode. There is a strong hybridization between cyano ligands and manganese-3d states, which benefits the electronic property for improving rate performance. Additionally, we employ an organic-aqueous cosolvent electrolyte to solve the long-standing solubility issue of Prussian blue analogs. A full-cell sodium-ion battery with low-cost Prussian blue analogs in both electrodes and co-solvent electrolyte retains 95% of its initial discharge capacity after 1000 cycles at 1C and 95% depth of discharge. The revealed manganese(I/II) redox couple inspires conceptual innovations of batteries based on atypical oxidation states.
Optimal Exhaust Valve Opening Control for Fast Aftertreatment Warm Up in Diesel Engines (2018)

This paper proposes to optimally adjust the exhaust valve opening (EVO) timing for faster selective catalytic reduction (SCR) aftertreatment system warm-up during the cold start phase of the federal test procedure (FTP). Early termination of the power stroke by EVO timing advance increases the engine exhaust gas temperature. It, on the other hand, causes exhaust flow rate reduction that decreases the coefficient of the heat transfer from the exhaust gas to the catalyst. The competing effects along with the fuel consumption increase associated with early EVO need careful consideration and the optimal EVO timing is a load-dependent balance of all these effects. This careful balance is achieved in this paper by dynamic programing (DP). Specifically, the minimum time to light-off (TTL) is formulated and applied to the cold phase of the FTP. A high fidelity detailed and verified engine and aftertreatment model is effectively simplified to enable utilizing computationally expensive DP optimization algorithm. Optimization results indicate that advancing the EVO reduces the TTL for the SCR catalyst from 659 s to 500 s, a 24% reduction. This fastest possible increase in the SCR temperature is shown to be with an expense of 4.1% increase in the fuel consumption. The results are dependent to the target light-off temperature and the load profile. Assuming a specific light-off temperature and the FTP, possible rule-based scenarios for online optimization are discussed.
Batch fabrication of thin film magnetic recording heads: A literature review and process description for vertical single turn heads (1975)

Several publications in the past have discussed the potential of batch fabricated thin film heads. Most of these publications dealt with theoretical predictions. Only a few discussed fabrication techniques and reported on the write and read test results. This paper describes a fabrication process for single turn thin film heads of vertical configuration. The process utilizes well known evaporation, plating, and photolithographic techniques. It is simple, inexpensive, and amenable to batch fabrication. Heads fabricated using this process were shown to write and read on a disk, moving at 40 m/s (1575 in/s) with ∼6 Kfr/cm. Dynamic test results reported in a paper by Valstyn and Shew corroborate the earlier prediction. This paper also discusses and compares advantages and disadvantages of the single turn heads of a vertical configuration with those of a horizontal configuration.
218-LB: Remission of Type 2 Diabetes after Weight Loss in "Normal" Weight People—The ReTUNE Study (2022)

Background and aims: Mechanisms underlying weight loss induced remission of type 2 diabetes (T2DM) have been reported only in people with BMI &amp;gt;27kg/m2. The Personal Fat Threshold hypothesis postulated that the same mechanisms in people with BMI &amp;lt;27kg/m2. Pathophysiology during stepwise dietary weight loss was studied in this group. Methods: People with T2DM (13/20 female, mean (±1SD) 59.3±7.1 years, BMI 24.8±1.7kg/m2) were studied before and after up to three 5% weight loss cycles, each comprising a 2-4 week low energy diet (800kcal/day formula meal replacements plus non starchy vegetables) , followed by 4-6 weeks of weight maintenance. All hypoglycemic agents were stopped before weight loss. Studies were repeated at 12 months. Outcomes were compared to normoglycemic matched controls (n=20) . Intrahepatic and intrapancreatic fat was quantified by magnetic resonance, and a standard meal test assessed insulin secretion by Disposition Index (DI) . Results: 70% achieved remission (HbA1c &amp;lt;6.5%; 14/20) , accompanied by decrease in adipose tissue distress (Median (IQR) PAI-1 8.64 (6.97-11.01) to 5.99 (3.94--7.73) p&amp;lt;0.02 [control 4.87 (3.49-7.03] ng/ml; GDF-15 591 (439-872) to 444 (395-554) [446 (383-614] pg/ml p&amp;lt;0.05. Between baseline and 12 months, decrease was (mean±SE; control data in square brackets) : BMI 24.8±0.4 to 22.5±0.4 kg/m2 (p&amp;lt;0.0001) [21.5±0.5]; total body fat 32.1±1.5 to 27.6±1.8% (p&amp;lt;0.0001) [24.6±1.5]; Fasting plasma insulin 47±6 to 24±6pmol/l (p&amp;lt;0.001) [23±2]; liver fat 4.0±0.6 to 1.6±0.2% (p=0.02) [1.9±0.3]; plasma triglycerides 1.4±0.2 to 0.9±0.1mmol/l (p&amp;lt;0.02) [0.9±0.1]; Intrapancreatic fat (6.1±0.5 to 5.0±0.6% (p=0.03) [4.1±0.3]. DI increased from median (IQR) 289 (183-373) to 774 (486-1709) dl/kg/min per pmol/l (p&amp;lt;0.05) but remained subnormal [2751 (1524-3526]. Conclusion: Mechanistic changes underpinning remission after weight loss in non-obese people with T2DM are the same as in obese people. T2DM occurs if a person becomes too heavy for their own constitution, irrespective of BMI. Weight loss of ∼10% can bring about T2DM remission in people classified as having a ‘normal’ BMI. Disclosure R. Taylor: Speaker's Bureau; Janssen Global Services, LLC, Lilly Diabetes, Nestlé Health Science, Novartis AG. C. Cobelli: None. K. M. Irvine: None. A. C. Barnes: None. T. L. Kelly: None. L. G. Clark: None. K. G. Hollingsworth: None. A. Al-mrabeh: None. R. R. Holman: Advisory Panel; Anji Pharmaceuticals, Novartis AG, Novo Nordisk, Consultant; AstraZeneca, Research Support; AstraZeneca, Bayer AG, Merck Sharp &amp; Dohme Corp. D. Romeres: None. Funding Diabetes UK (17/0005645)
Enhancing the flexibility and functionality of SCNs: demonstration of evolution toward any-core-access, nondirectional, and contentionless spatial channel cross-connects [Invited] (2021)

A spatial channel network (SCN) was recently proposed toward the forthcoming spatial division multiplexing (SDM) era, in which the optical layer is explicitly evolved to the hierarchical SDM and wavelength division multiplexing layers, and an optical node is decoupled into a spatial cross-connect (SXC) and wavelength cross-connect to achieve an ultrahigh-capacity optical network in a highly economical manner. In this paper, we report feasibility demonstrations of an evolution scenario regarding the SCN architecture to enhance the flexibility and functionality of spatial channel networking from a simple fixed-core-access and directional spatial channel ring network to a multidegree, any-core-access , nondirectional , and core-contentionless mesh SCN. As key building blocks of SXCs, we introduce what we believe to be novel optical devices: a <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>1</mml:mn> </mml:mrow> <mml:mo>×</mml:mo> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>2</mml:mn> </mml:mrow> </mml:math> multicore fiber (MCF) splitter, a core selector (CS), and a core and port selector (CPS). We construct free-space optics-based prototypes of these devices using five-core MCFs. Detailed performance evaluations of the prototypes in terms of the insertion loss (IL), polarization-dependent loss (PDL), and intercore cross talk (XT) are conducted. The results show that the prototypes provide satisfactorily low levels of IL, PDL, and XT. We construct a wide variety of reconfigurable spatial add/drop multiplexers (RSADMs) and SXCs in terms of node degree, interport cross-connection architecture, and add/drop port connectivity flexibilities. Such RSADMs/SXCs include a fixed-core-access and directional RSADM using a <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>1</mml:mn> </mml:mrow> <mml:mo>×</mml:mo> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>2</mml:mn> </mml:mrow> </mml:math> MCF splitter; an any-core-access, nondirectional SXC with core-contention using a CS; and an any-core-access, nondirectional SXC without core-contention using a CPS. Bit error rate performance measurements for SDM signals that traverse the RSADMs/SXCs confirm that there is no or a very slight optical signal-to-noise-ratio penalty from back-to-back performance. We also experimentally show that the flexibilities in the add/drop port of the SXCs allow us to recover from a single or concurrent double link failure with a wide variety of options in terms of availability and cost-effectiveness.
Increasing the Landscape of Structural Motifs in Co-crystals of Resorcinols with Ditopic Aromatics: A One-dimensional π-Stacked Hydrogen-Bonded Polymer Involving a Phenanthroline (2006)

Co-crystals involving 4,6-dichlororesorcinol (4,6-diCl-res) and 2,9-phenanthroline (2,9-phen) of composition 2(4,6-diCl-res) ··· 2(2,9-phen) ··· (nitromethane) ( 1 ) reveal a previously unobserved one-dimensional structural motif that involves a π-stacked columnar polymer held together by O–H···N hydrogen bonds. Each resorcinol participates in short Cl···O contacts and Cl···Cl forces along the polymer backbone. The included nitromethane solvent molecules pack in columns held together by C–H···O forces.
Activation of Stat 5b in erythroid progenitors correlates with the ability of ErbB to induce sustained cell proliferation. (1996)

Self renewal of normal erythroid progenitors is induced by the receptor tyrosine kinase c-ErbB, whereas other receptors (c-Kit/Epo-R) regulate erythroid differentiation. To address possible mechanisms that could explain this selective activity of c-ErbB, we analyzed the ability of these receptors to activate the different members of the Stat transcription factor family. Ligand activation of c-ErbB induced the tyrosine phosphorylation, DNA-binding, and reporter gene transcription of Stat 5b in erythroblasts. In contrast, ligand activation of c-Kit was unable to induce any of these effects in the same cells. Activation of the erythropoietin receptor caused specific DNA-binding of Stat 5b, but failed to induce reporter gene transcription. These biochemical findings correlate perfectly with the selective ability of c-ErbB to cause sustained self renewal in erythroid progenitors.
Tolerance of cotton expressing a 2,4-D detoxification gene to 2,4-D applied in the field (2007)

The tolerance to 2,4-dichlorophenoxy acetic acid (2,4-D) of a genetically modified (transgenic) cotton (Gossypium hirsutum) expressing a 2,4-D detoxification gene was compared with conventional (non-transgenic) cotton over 2 seasons. The 2,4-D was applied over-the-top of cotton in the field at 7–17 nodes of crop growth at rates of 0.004–1.12 kg a.i./ha. The transgenic cotton displayed better tolerance to 2,4-D than conventional cotton at all growth stages and herbicide rates. Some damage was apparent on both types of cotton at 2,4-D rates of 0.07 kg/ha and above, with damage most pronounced when the plants were exposed at 7 nodes. The transgenic cotton also had some tolerance to MCPA. Commercial use of transgenic, 2,4-D-tolerant cotton has the potential to greatly reduce problems of 2,4-D damage in cotton from accidental spray drift and herbicide residues in spraying equipment, where plants are predominantly exposed to low rates of 2,4-D.