gebhart/patrepeval huggingface dataset:
Rosenbrock schemes with complex coefficients for stiff and differential algebraic systems (2006)

Many applied problems are described by differential algebraic systems. Complex Rosenbrock schemes are proposed for the numerical integration of differential algebraic systems by the ɛ-embedding method. The method is proved to converge quadratically. The scheme is shown to be applicable even to superstiff systems. The method makes it possible to perform computations with a guaranteed accuracy. An equation is derived that describes the leading term of the error in the method as a function of time. An algorithm extending the method to systems of differential equations for complex-valued functions is proposed. Examples of numerical computations are given.
Molecular characterization of an improved vector for evaluation of the tumor suppressor versus oncogene abilities of the androgen receptor (2004)

These pSG5-AR versus pSAR-IRES-EGFP clones are being studied to determine the molecular pathways explaining their different response to AR and ligand.
“Magnet-in-the-Semiconductor” FePt−PbS and FePt−PbSe Nanostructures: Magnetic Properties, Charge Transport, and Magnetoresistance (2010)

We report a synthesis of colloidal nanostructures combining a magnetic material (FePt) with a narrow-gap semiconductor (PbS and PbSe) in form of core-shells or nanodumbbells and explore their optical, magnetic, electrical, and magnetotransport properties. The arrays of "magnet-in-the-semiconductor" nanostructures show semiconductor-type transport properties with magnetoresistance typical for magnetic tunnel junctions, thus combining the advantages of both functional components. We observed gate-controlled charge transport through the arrays of FePt-PbS and FePt-PbSe core-shell nanostructures with an electron mobility of 0.01 cm(2)/(V s) and 0.08 cm(2)/(V s), respectively, combined with ferro- and superparamagnetic behavior and large tunneling magnetoresistance. This work shows that multicomponent colloidal nanostructures can be used as the building blocks for design of multifunctional materials for electronics and optoelectronics.
Human Amylin Oligomer Growth and Fibril Elongation Define Two Distinct Phases in Amyloid Formation (2004)

Human amylin (hA), a 37-amino-acid polypeptide, is one of a number of peptides with the ability to form amyloid fibrils and cause disease. It is the main constituent of the pancreatic amyloid deposits associated with type 2 diabetes. Increasing interest in early assembly intermediates rather than the mature fibrils as the cytotoxic agent has led to this study in which the smallest hA oligomers have been captured by atomic force microscopy. These are 2.3 +/- 1.9 nm in height, 23 +/- 14 nm in length, and consist of an estimated 16 hA molecules. Oligomers first grow to a height of about 6 nm before they begin to significantly elongate into fibrils. Congo red inhibits elongation but not the growth in height of hA oligomers. Two distinct phases have thus been identified in hA fibrillogenesis: lateral growth of oligomers followed by longitudinal growth into mature fibrils. These observations suggest that mature fibrils are assembled directly via longitudinal growth of full-width oligomers, making assembly by lateral association of protofibrils appear less likely.
Quantitative Subtyping of Hepatitis B Virus Reveals Complex Dynamics of Ymdd Motif Mutants Development during Long-Term Lamivudine Therapy (2006)

Mass spectrometry is an accurate and cheap method for the detection of YMDD mutants, even in the presence of overwhelming wild-type HBV. We observed some intriguing mutant viral dynamics during 3TC treatment. Further studies are needed to clarify whether they have any clinical significance.
The impact of volume overload on technique failure in incident peritoneal dialysis patients (2019)

Volume overload at start of PD and/or at 6 months was associated with a higher risk of technique failure in the subsequent year. The risk was modified by centre characteristics, which varied among regions.
Lightweight software transactions for games (2009)

To realize the performance potential of multiple cores, soft-ware developers must architect their programs for concur-rency. Unfortunately, for many applications, threads and locks are difficult to use efficiently and correctly. Thus, re-searchers have proposed transactional memory as a simpler alternative. To investigate if and how software transactional mem-ory (STM) can help a programmer to parallelize applica-tions, we perform a case study on a game application called SpaceWars3D. After experiencing suboptimal performance, we depart from classic STM designs and propose a program-ming model that uses long-running, abort-free transactions that rely on user specifications to avoid or resolve conflicts. With this model we achieve the combined goal of competi-tive performance and improved programmability. 1.
[Pathological effects of recently isolated complement derived peptides]. (1982)

The C3a and C5a polypeptides release, under conditions of complement activation, causes a change in PMN shape and adhesiveness with formation of leukoemboli in microvascular districts. Those modified granulocytes produce oxygen radicals with toxic activity. This mechanism seems to play a role in different pathological situations like pulmonary distress in hemodialysis, leukapheresis, cardiopulmonary by-pass and extent of necrosis in acute myocardial infarction. The same mechanism has been largely investigated in Adult Respiratory Distress Syndrome (A.R.D.S.). In this condition the leukoembolization toxicity seems to be the most important pathogenetic factor of the alveolo-capillary membrane damage which is the base of the disease.
Determinants of Stress Shielding (1992)

Experimental studies of cementless porous-coated total hip arthroplasty indicate that a critical design variable for femoral remodeling is stem stiffness. In the long term (two years) in the canine model, other variables, including the presence, type, and placement of the porous coating, did not significantly affect the pattern of bone remodeling when tested with metallic stems. The basic pattern of bone remodeling was characterized by proximal cortical atrophy, and distal cortical and medullary bone hypertrophy. In the short term (six months), the use of low-stiffness stems altered this pattern, leading to reduced proximal bone loss, increased proximal medullary bone hypertrophy, and no distal cortical hypertrophy, suggesting that stem stiffness had a profound effect on stress shielding.
309. Optimization of Production of AAVrh.10 Viral Vectors (2016)

With the increasing interest in the use of adeno-associated virus (AAV) vectors to treat human disorders, there is increasing focus on optimizing AAV production to improve yield, purity and potency. The production of AAV vectors can be conceptualized in two stages: upstream cell culture and downstream purification and formulation. As an example of how AAV production can be optimized, we assessed upstream (cell density at transfection, plasmid and transfection reagent concentration, cell culture nutrients and harvest timing) and downstream (virus recovery, purification methods, potency) steps in the production of AAVrh. 10, a nonhuman primate vector, using adherent 293T cells and a 2 plasmid transfection system using polyethylenimine (PEI). Upstream, vector yield, as measured by quantitative PCR in the cell harvest from transfections at each of several different cell densities peaked at 8 × 104 cell/cm2. Total vector yield as a function of time after transfection peaked at day 3 post-transfection with diminishing returns and greater partitioning into the cell supernatant at longer times. Higher vector yield correlated with a greater total quantity of plasmid and PEI, but changing the PEI:plasmid ratio from 1:1 diminished productivity. Fetal bovine serum concentration had minimal effect. Downstream, freeze-thaw methods were not reproducible. Physically lysing the cells was not as effective for AAV recovery as the detergents, triton or tween, which were equally effective, with the lowest effective detergent concentration important to minimize the residual detergent in the final product. While iodixanol gradients are the traditional AAV purification systems, depth filtration followed by tangential flow filtration worked well for small scale production (>90%), but for large scale was less efficient (>70%). Affinity chromatography using AVB (GE Healthcare Life Sciences), provided an effective purification with maximum vector loads of up to 3 × 1012 vector genomes per ml of packed column. Finally, concentration of the final bulk AAV product was critically dependent on a formulation that stabilizes the solubility of the AAV monomer, with 0.01% pluronic acid providing AAV recovery of nearly 80%. Together, the optimized methods for the best yield, purity and potency relied on transfection with equal amounts of plasmid and PEI and a cell density of 8 × 104 cells/cm2 combined with the use of detergent to disrupt and recover AAV and sequential purification by depth filtration, tangential flow filtration and affinity chromatography. This process improved the yield from harvest to final product from 9% to 40% and achieved final purified AAV at 7 × 109 vector genomes/cm2 of adherent cell culture. These systematic refinements to the individual steps of AAV production demonstrate improved yield and facilitates transfer of a method for GMP production for clinical use.
Magnetotransport Properties across Verwey Transition in Fe3O4(111) Epitaxial Thin Films (2013)

We have studied the magnetoresistance (MR) of high-quality Fe3O4 thin films across the Verwey transition temperature (TV). Different from unsaturated MR observed in many other Fe3O4 films, MR of the present film at a high magnetic field is almost independent of the field, consistent with the fully saturated magnetization. The MR at low field strongly depends on temperature and orientation around TV: While out-of-plane MR sharply decreases from ∼+7 to ∼-5%, in-plane MR abruptly increases from ∼-6 to ∼+3% on cooling across TV.
Treatment of chronic delta hepatitis with lamivudine vs lamivudine + interferon vs interferon (2008)

Chronic delta hepatitis is the most severe form of chronic viral hepatitis for which interferon (IFN) is the only available treatment. In 39 patients (25 were treatment-naïve, 14 had previously used IFN), efficacy of 1-year treatment with IFN (9 MU, t.i.w.) or lamivudine (LAM; 100 mg, q.d.) alone was compared with IFN and LAM combination (2 months of LAM to be followed by combination treatment). IFN monotherapy was given only to treatment-naïve patients. In both treatment-naïve and previous IFN users, end of treatment virological and biochemical responses were similar with IFN-LAM combination and superior to LAM monotherapy (P < 0.05). Improvement in liver histology occurred more often with IFN +/- LAM than with LAM alone (P < 0.05). In treatment-naïve patients, combination treatment was not superior to IFN monotherapy. After treatment discontinuation, virological and biochemical response rates decreased in LAM and IFN combination and IFN monotherapy. On treatment virological response at month 6 of treatment predicted sustained virological response. The results of this study suggest that addition of LAM to IFN for the treatment of delta hepatitis is of no additional value and that both treatment modalities are superior to LAM monotherapy.
Solvent-free autocatalytic supramolecular polymerization (2021)

Abstract Solvent-free chemical manufacturing is one of the awaited technologies for addressing an emergent issue of serious environmental pollution. Here, we report "solvent-free autocatalytic supramolecular polymerization (SF-ASP)", where a phthalonitrile derivative with hydrogen-bonding side chains as the monomer is autocatalytically transformed into the corresponding phthalocyanine in an exceptionally high yield (&gt; 80%). The target phthalocyanine, if any is produced, nucleates and initiates supramolecular polymerization via a hydrogen-bonding interaction, affording one-dimensional single-crystalline fibers. These crystalline fibers possibly preorganize the precursor phthalonitrile monomer at their cross-sectional edges and autocatalytically convert them into the phthalocyanine under out-of-equilibrium conditions. In the presence of metal oleates, SF-ASP autocatalytically affords single-crystalline fibers of metallophthalocyanines again in exceptionally high yields. In these cases, such fibers grow in both directions without terminal coupling until the precursor phthalonitrile is completely consumed. By taking advantage of this quasi-living character of polymerization, multistep SF-ASP without/with metal oleates affords multi-block supramolecular copolymers.
Capacitor loading equipment module (CLEM) operation manual (1977)

The purpose of this manual is to provide the necessary information to safely operate and maintain the capacitor loading equipment module designed and built by EG&G, Inc. for the Lawrence Livermore Laboratory Shiva Laser System. The system consist of two primary pieces of equipment: a Clark forklift and the Platform Assembly (CLEM). The fork-lift transports CLEM to and from capacitor module racks and repair/storage areas, and provides 24-volt d-c power to CLEM. The CLEM system is used to place or remove capacitor modules to or from shelves and provides a platform for transport. Capacitor modules are approximately 15 in. high and 30 in. deep. The widths and weights range from 42 in. to 75 in. and 600 lb. to 1125 lb., respectively. The storage racks are 7 shelves high and spaced 20.5 in. apart. The fourth through seventh shelf are considered the upper level. CLEM also has a manlift and remote control station to provide the operator access to capacitor modules on shelves higher than S feet. The CLEM platform translates right and left from the center position to the shelf. A drawbar, which pulls a capacitor module onto the platform or pushes the module from the platform onto the shelf, translates the full width of the platform. Capacitor modules can be handled from either side of CLEM. Maximum-load and critical data are listed on a name plate attached to CLEM. CLEM is finished with a durable, baked-on epoxy powder coating.
K band very low noise DRO (2002)

In this paper we present the design and performance of a K band DRO (Dielectric Resonator Oscillator). The design incorporates NE71000 MESFET and an open source oscillator topology, which we show to be superior in terms of bandwidth and noise. The same circuit can be used (with different resonators) in the frequency range 21-25 GHz. The output power is 10 dbm, frequency stability 4 ppm/degree C and phase noise -88 dbc/Hz@10 kHz (several db better compared to previously published DROs at this frequency range).
Production of Vascular Endothelial Growth Factors from Human Lung Macrophages Induced by Group IIA and Group X Secreted Phospholipases A2 (2010)

Angiogenesis and lymphangiogenesis mediated by vascular endothelial growth factors (VEGFs) are main features of chronic inflammation and tumors. Secreted phospholipases A(2) (sPLA(2)s) are overexpressed in inflammatory lung diseases and cancer and they activate inflammatory cells by enzymatic and receptor-mediated mechanisms. We investigated the effect of sPLA(2)s on the production of VEGFs from human macrophages purified from the lung tissue of patients undergoing thoracic surgery. Primary macrophages express VEGF-A, VEGF-B, VEGF-C, and VEGF-D at both mRNA and protein level. Two human sPLA(2)s (group IIA and group X) induced the expression and release of VEGF-A and VEGF-C from macrophages. Enzymatically-inactive sPLA(2)s were as effective as the active enzymes in inducing VEGF production. Me-Indoxam and RO092906A, two compounds that block receptor-mediated effects of sPLA(2)s, inhibited group X-induced release of VEGF-A. Inhibition of the MAPK p38 by SB203580 also reduced sPLA(2)-induced release of VEGF-A. Supernatants of group X-activated macrophages induced an angiogenic response in chorioallantoic membranes that was inhibited by Me-Indoxam. Stimulation of macrophages with group X sPLA(2) in the presence of adenosine analogs induced a synergistic increase of VEGF-A release and inhibited TNF-alpha production through a cooperation between A(2A) and A(3) receptors. These results demonstrate that sPLA(2)s induce production of VEGF-A and VEGF-C in human macrophages by a receptor-mediated mechanism independent from sPLA(2) catalytic activity. Thus, sPLA(2)s may play an important role in inflammatory and/or neoplastic angiogenesis and lymphangiogenesis.
The potential of double recirculating aquaponic systems for intensive tomato production (2019)

Aquaponics combine the production of fish and plants in a sustainable way due to the double use of water and nutrients. Compared to conventional single recirculation aquaponic systems (SRAPS), the double recirculation aquaponic systems (DRAPS) are improved by the combination of two separate recirculating systems: the recirculating aquaculture system (RAS) for fish rearing and a closed hydroponic cycle for plant production. Both systems are connected in one direction to transfer the nutrient rich fish waste water to the hydroponic unit. The unidirectional connection of both systems allows the optimisation of fish waste water for plant growth by addition of mineral fertilizer without negative effects on fish rearing. DRAPS is a relative new approach and information about the functionality and successful use are rare. Therefore, more research on DRAPS is necessary. The present study was focused on different growth and production parameters of tomatoes produced in DRAPS compared to those produced in conventional hydroponics. Investigations during an annual production in 2015 showed that tomatoes produced in DRAPS have a comparable plant growth and development as obtained for conventional hydroponics. Even the fruit quantity and the fruit quality, including nutrient contents, were similar in both production systems.
Data from DCAMKL-1 Regulates Epithelial–Mesenchymal Transition in Human Pancreatic Cells through a <i>miR-200a</i>–Dependent Mechanism (2023)

&lt;div&gt;Abstract&lt;p&gt;Pancreatic cancer is an exceptionally aggressive disease in great need of more effective therapeutic options. Epithelial–mesenchymal transition (EMT) plays a key role in cancer invasion and metastasis, and there is a gain of stem cell properties during EMT. Here we report increased expression of the putative pancreatic stem cell marker DCAMKL-1 in an established KRAS transgenic mouse model of pancreatic cancer and in human pancreatic adenocarcinoma. Colocalization of DCAMKL-1 with vimentin, a marker of mesenchymal lineage, along with 14-3-3 σ was observed within premalignant PanIN lesions that arise in the mouse model. siRNA-mediated knockdown of DCAMKL-1 in human pancreatic cancer cells induced microRNA &lt;i&gt;miR-200a&lt;/i&gt;, an EMT inhibitor, along with downregulation of EMT-associated transcription factors ZEB1, ZEB2, Snail, Slug, and Twist. Furthermore, DCAMKL-1 knockdown resulted in downregulation of c-Myc and KRAS through a &lt;i&gt;let-7a&lt;/i&gt; microRNA-dependent mechanism, and downregulation of Notch-1 through a &lt;i&gt;miR-144&lt;/i&gt; microRNA-dependent mechanism. These findings illustrate direct regulatory links between DCAMKL-1, microRNAs, and EMT in pancreatic cancer. Moreover, they demonstrate a functional role for DCAMKL-1 in pancreatic cancer. Together, our results rationalize DCAMKL-1 as a therapeutic target for eradicating pancreatic cancers. &lt;i&gt;Cancer Res; 71(6); 2328–38. ©2011 AACR.&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Regulation of Neurosteroid Biosynthesis by Neurotransmitters and Neuropeptides (2012)

The enzymatic pathways leading to the synthesis of bioactive steroids in the brain are now almost completely elucidated in various groups of vertebrates and, during the last decade, the neuronal mechanisms involved in the regulation of neurosteroid production have received increasing attention. This report reviews the current knowledge concerning the effects of neurotransmitters, peptide hormones, and neuropeptides on the biosynthesis of neurosteroids. Anatomical studies have been carried out to visualize the neurotransmitter- or neuropeptide-containing fibers contacting steroid-synthesizing neurons as well as the neurotransmitter, peptide hormones, or neuropeptide receptors expressed in these neurons. Biochemical experiments have been conducted to investigate the effects of neurotransmitters, peptide hormones, or neuropeptides on neurosteroid biosynthesis, and to characterize the type of receptors involved. Thus, it has been found that glutamate, acting through kainate and/or AMPA receptors, rapidly inactivates P450arom, and that melatonin produced by the pineal gland and eye inhibits the biosynthesis of 7α-hydroxypregnenolone (7α-OH-Δ(5)P), while prolactin produced by the adenohypophysis enhances the formation of 7α-OH-Δ(5)P. It has also been demonstrated that the biosynthesis of neurosteroids is inhibited by GABA, acting through GABA(A) receptors, and neuropeptide Y, acting through Y1 receptors. In contrast, it has been shown that the octadecaneuropetide ODN, acting through central-type benzodiazepine receptors, the triakontatetraneuropeptide TTN, acting though peripheral-type benzodiazepine receptors, and vasotocin, acting through V1a-like receptors, stimulate the production of neurosteroids. Since neurosteroids are implicated in the control of various neurophysiological and behavioral processes, these data suggest that some of the neurophysiological effects exerted by neurotransmitters and neuropeptides may be mediated via the regulation of neurosteroid production.
Vehicle heading estimation of INS/magnetometer integrated system based on constant hard iron interference calibration (2021)

The integrated INS/magnetometer measurement is widely used in low-cost navigation systems. The integration has proven more effective in suppressing the divergence of heading than relying solely on a magnetometer because this is susceptible to local magnetic field interference, reducing heading accuracy. Magnetometers sense the local magnetic field that may be interfered by the nearby ferromagnetic material or strong electric currents. Hence, the magnetometer must be calibrated in the vehicle before use. When a magnetometer is installed near power components (engines, etc.), soft iron interference can be ignored. In the vehicle’s external environment, the time-varying hard iron interference can reach 100 times the strength of the geomagnetic field, meaning that a magnetometer cannot function efficiently because its accuracy is so reduced. Hence, the constant hard magnetic interference inside the vehicle is mainly concerned in this paper. An INS/Magnetometer heading estimation algorithm based on a two-stage Kalman filter is proposed to solve the problem by combining inertial sensor and magnetometer with attitude information. In the first stage filter, the constant hard iron interference is estimated by setting upward standing the three IMU axes. In the second stage filter, the INS/Magnetometer heading estimation is implemented. Finally, the results show that the algorithm improves the accuracy of vehicle heading calculations.
Genomic library construction (2023)

Compositions and methods for amplifying nucleic acid sequences from a single cell are provided. Compositions and methods for constructing a genomic library from a single cell are also provided.