gebhart/patrepeval huggingface dataset:
The Atmospheric Radiation Measurement Program and interfaces with external data sources (1993)

The Atmospheric Radiation Measurement (ARM) Program is the Department of Energy`s major field project in support of its global change research program. Its objective is to improve the performance of cloud and radiation models and parameterizations in general circulation models (GCMs) used for climate research. The data produced by ARM will be handled and maintained to satisfy the research needs of the program and to be accessible and usable by the general research and academic communities. In addition to data from field instrumentation, ARM Science Team needs include a substantial amount of data from outside the ARM Program (``external data``), which will be acquired and provided routinely through the ARM data system. With respect to data archival and sharing, the ARM Program reflects the objectives delineated by the US Global Change. The purpose of this presentation is to summarize the conceptual designs embodied in the ARM data system and the status of its implementation.
Magnetic Nanocrescents as Controllable Surface‐Enhanced Raman Scattering Nanoprobes for Biomolecular Imaging (2005)

Magnetic nanocrescent Raman probes (see Figure) can not only serve as stand-alone surface-enhanced Raman scattering (SERS) substrates with high local electromagnetic-field enhancement factors, but can also be controlled by external magnetic fields to produce translational and rotational motion of the nanoprobes. Their near-IR optical activities may be useful for biomedical imaging, as near-IR radiation results in deeper tissue penetration and minimal photothermal damage. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2005/c1064_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
SAT-219 A Novel 1-Year Contraceptive Vaginal System Delivering Segesterone Acetate and Ethinyl Estradiol: Effects on Lipids and other Hepatic Proteins (2019)

Annovera™ is an FDA-approved contraceptive vaginal system (CVS) releasing 150 mcg segesterone acetate (SA), a new chemical entity, and 13 mcg ethinyl estradiol (EE) per day.1 We postulate that as a non-androgenic progestin, SA is unlikely to adversely affect lipids versus androgenic progestins. Here we review the effects of this CVS on lipids, glucose, coagulation factors and sex hormone-binding globulin (SHBG). Two pivotal, open-label, phase 3 trials and one PK trial evaluated women (18-40 years) who received the CVS for 13 cycles of 28 days over 12 months; one phase 3 study examined hepatic proteins in a substudy. The CVS was self-inserted, left in place for 21 days and removed for 7 days in each 28-day cycle. Lipids and glucose were measured at baseline and study end in the 3 trials. As previously reported, factor VIII, protein S (PS), fibrinogen, and SHBG were measured in the hepatic factors substudy.2 A total of 2308 women used the SA/EE CVS. Participants had a mean age of 26.7 years and mean BMI of 24.1 kg/m2. Most women were white (71%) and 14% were black. Women in the substudy (n=129) had similar mean ages and BMIs; 69% were white and 28% were black. In an integrated analysis of the phase 3 and PK studies, levels of total cholesterol increased by a mean +0.236 mmol/L from baseline to study end, as did HDL cholesterol (+0.162 mmol/L) and triglycerides (+0.193 mmol/L). At study end, LDL cholesterol decreased from baseline by a mean of -0.003 mmol/L. Glucose levels increased from baseline to study end by a mean +0.074 mmol/L. A prior study using the CVS showed lipid changes similar in direction and magnitude to other combined oral contraceptives (COC).3 Hepatic protein substudy results showed significant mean changes from baseline to study end for fibrinogen (+0.2±0.66 mg/mL [SD]; P=0.0052), factor VIII activity (+21%±55; P=0.0005), and PS activity (-8%±19; P=0.0043). Mean SHBG levels also significantly increased from baseline to study end by +81.7±94.3 nmol/L (P<0.0001).2 Another study comparing the CVS to an oral COC showed that the CVS had a hemostatic profile corresponding closely with that of the oral COC.4 Integrated safety data from two clinical studies, a hepatic substudy from one of the trials, and prior reports showed no clinically significant impact of the SA/EE CVS on lipids or glucose. The impact of the CVS on coagulation factors mirrored that of oral COCs. The significant increase in SHBG levels with the CVS was consistent with changes seen with other COCs containing EE and a non-androgenic progestin. The SA/EE CVS with a low dose of EE and the novel progestin, SA, has an acceptable metabolic profile with up to one year of use. 1. AnnoveraTM Prescribing Information. 2. Archer DF, et al. Contraception 2016;93(1):58-64. 3. Sitruk-Ware RL, et al. Contraception 2007;75(6):430-437. 4. Rad M, et al. Am J Obstet Gynecol 2006;195(1):72-77.
Immunity to coccidiosis: T-lymphocyte- or B-lymphocyte-deficient animals (1979)

Comparisons were made between infections with Eimeria spp. in normal animals and in animals with functional deficiencies in either T-lymphocytes (athymic nude rats) or B-lymphocytes (bursectomized chickens). Approximately three times more oocysts of E. nieschulzi were passed during a primary infection in the nu/nu rats, and in contrast to the nu/+ rats, they were completely susceptible to reinfection. Nu/nu rats did not produce agglutinating antibodies to sporozoites, and injections of serum from immunized nu/+ rats caused a reduction of oocyst production during a primary infection in both nu/nu and nu/+ rats. In chickens, oocyst production in primary infections with E. maxima or with E. acervulina was increased 1.5 to 2-fold in the bursectomised (BX) groups, and the clinical effects of infection with E. maxima were greater than in controls. The BX birds were slightly more susceptible than the controls to challenge inoculations of oocysts, but nevertheless, they were very substantially immune. Tests for the functioning of B- and T-lymphocytes indicated that in the BX birds there was a severe deficiency of B-cell function, but near-normal T-cell function. The results show that T-lymphocytes are essential for immunity and that, although they may function partly as helper cells for immunoglobulin production, their major effect is exerted via some other mechanism.
Seeded propagation of alpha-synuclein aggregation in mouse brain using protein misfolding cyclic amplification (2019)

Alpha-synuclein (α-syn) protein aggregation is associated with several neurodegenerative disorders collectively referred to as synucleinopathies, including Parkinson disease. We used protein misfolding cyclic amplification (PMCA) to study α-syn aggregation in brain homogenates of wild-type or transgenic mice expressing normal (D line) or A53T mutant (M83 line) human α-syn. We found that sonication-incubation cycles of M83 mouse brain gradually produce large quantities of SDS-resistant α-syn aggregates, involving both human and mouse proteins. These PMCA products, containing partially proteinase K resistant α-syn species, are competent to accelerate the onset of neurological symptoms after intracerebral inoculation to young M83 mice and to seed aggregate formation of α-syn following PMCA, including in D and wild-type mouse brain substrates. Our data indicate that similar to prions, PMCA can reproduce some characteristics of α-syn aggregation and seeded-propagation in vitro in a complex milieu. This opens new opportunities for the molecular study of synucleinopathies.
Temporal Patterns of Gene Expression Profiles in the Neonatal Mouse Lung after Hypoxia-Reoxygenation (2016)

In this newborn mouse lung hypoxia-reoxygenation model, we found downregulation of genes of mediators of inflammation, an antiapoptotic gene expression pattern, and downregulation of DNA glycosylases. Sod1 and Il1b were significantly differentially expressed when comparing reoxygenation using 60% O2 with air.
Efficacy of the Combination of Metformin and CTLA4Ig in the (NZB × NZW)F1 Mouse Model of Lupus Nephritis (2020)

CTLA4Ig, a reagent that inhibits CD28 signaling, has shown therapeutic efficacy in mouse models of lupus nephritis (LN) when combined with several other biologics or standard of care drugs. Unfortunately, clinical trials treating LN patients with CTLA4Ig (abatacept) have not met endpoints. Metformin, a drug used to control hyperglycemia that inhibits mitochondrial metabolism, lowered the effective dose of glucocorticoids and prevented major flares when added on to the standard of care treatment of lupus patients with low disease activity. Metformin combined with inhibition of glycolysis by 2-deoxyglucose showed therapeutic efficacy in multiple mouse models of LN. Because CD28 signaling triggers glucose metabolism in T cells, we hypothesized that combining CTLA4Ig treatment with metformin would have the same effect. In this study, we showed that the combination of metformin and CTLA4Ig decreased the development of LN in (NZB × NZW)F1 mice treated at the early stage of disease. This preventive effect was associated with a decreased expansion of CD4<sup>+</sup> T cell effector subsets. However, contrary to the combination with 2-deoxyglucose, metformin combined with CTLA4Ig did not alter autoantibody production, suggesting different mechanisms of symptom mitigation. Overall, this study shows therapeutic efficacy of the combination of metformin and CTLA4Ig, two drugs with established safety records, in a preclinical mouse model of LN.
Vectorized mixed radix discrete Fourier transform algorithms (1987)

A number of previous attempts at the vectorization of the fast Fourier transform (FFT) algorithm have fallen somewhat short of achieving the full potential speed of vector processors. The algorithm formulation and implementation described here not only achieves full vector utilization but successfully copes with the problems of hierarchical storage. In the present paper, these techniques are described and extended to the general mixed radix algorithms, prime factor algorithm (PFA), the multidimensional discrete Fourier transform (DFT), the rectangular transform convolution algorithms, and the Winograd fast Fourier transform algorithm. Some of the methods were used in the Engineering Scientific Subroutine Library for the IBM 3090 Vector Facility. Using this approach, very good and consistent performance was obtained over a very wide range of transform lengths.
Sub-aperture EUV collector with dual-wavelength spectral purity filter (2015)

The combination of a 10.6 μm main pulse CO<sub>2 </sub>laser and a 1064 nm pre-pulse Nd:YAG laser in EUV source concepts for HVM would require collector mirrors with an integrated spectral purity filter that suppresses both laser wavelengths. This paper discusses a new approach of a dual-wavelength spectral purity filter to suppress 10.6 μm and 1064 nm IR radiation at the same time. The dual-wavelength spectral purity filter combines two binary phase gratings that are optimized for 10.6 μm and 1064 nm, respectively. The dual phase grating structure has been realized on spherical sub-aperture EUV collector mirrors having an outer diameter of 150 mm. IR suppression factors of 260 at 10.6 μm and 620 at 1064 nm have been measured on the sub-aperture EUV collector while its EUV reflectance exceeded 64 % at 13.5 nm.
Table S1 from Inhibin Is a Novel Paracrine Factor for Tumor Angiogenesis and Metastasis (2023)

&lt;p&gt;Quantification of parameters in the ovarian tissue array&lt;/p&gt;
Oncogenic Forms of NOTCH1 Lacking Either the Primary Binding Site for RBP-Jκ or Nuclear Localization Sequences Retain the Ability to Associate with RBP-Jκ and Activate Transcription (1997)

Truncated forms of the NOTCH1 transmembrane receptor engineered to resemble mutant forms of NOTCH1 found in certain cases of human T cell leukemia/lymphoma (T-ALL) efficiently induce T-ALL when expressed in the bone marrow of mice. Unlike full-sized NOTCH1, two such truncated forms of the protein either lacking a major portion of the extracellular domain (DeltaE) or consisting only of the intracellular domain (ICN) were found to activate transcription in cultured cells, presumably through RBP-Jkappa response elements within DNA. Both truncated forms also bound to the transcription factor RBP-Jkappa in extracts prepared from human and murine T-ALL cell lines. Transcriptional activation required the presence of a weak RBP-Jkappa-binding site within the NOTCH1 ankyrin repeat region of the intracellular domain. Unexpectedly, a second, stronger RBP-Jkappa-binding site, which lies within the intracellular domain close to the transmembrane region and significantly augments association with RBP-Jkappa, was not needed for oncogenesis or for transcriptional activation. While ICN appeared primarily in the nucleus, DeltaE localized to cytoplasmic and nuclear membranes, suggesting that intranuclear localization is not essential for oncogenesis or transcriptional activation. In support of this interpretation, mutation of putative nuclear localization sequences decreased nuclear localization and increased transcriptional activation by membrane-bound DeltaE. Transcriptional activation by this mutant form of membrane-bound DeltaE was approximately equivalent to that produced by intranuclear ICN. These data are most consistent with NOTCH1 oncogenesis and transcriptional activation being independent of association with RBP-Jkappa at promoter sites.
Quantitative Analysis of Protein–Protein Interactions (2004)

Numerous authors, including contributors to this volume, have described methods to detect protein-protein interactions. Many of these approaches are now accessible to the inexperienced investigator thanks to core facilities and/or affordable instrumentation. This chapter discusses some common design considerations that are necessary to obtain valid measurements, as well as the assumptions and analytical methods that are relevant to the quantitation of these interactions.
Translational Control of Putative Protooncogene Nm23-M2 by Cytokines via Phosphoinositide 3-Kinase Signaling (2004)

The expansion and differentiation of hematopoietic progenitors is regulated by cytokine and growth factor signaling. To examine how signal transduction controls the gene expression program required for progenitor expansion, we screened ATLAS filters with polysome-associated mRNA derived from erythroid progenitors stimulated with erythropoietin and/or stem cell factor. The putative proto-oncogene nucleoside diphosphate kinase B (ndpk-B or nm23-M2) was identified as an erythropoietin and stem cell factor target gene. Factor-induced expression of nm23-M2 was regulated specifically at the level of polysome association by a phosphoinositide 3-kinase-dependent mechanism. Identification of the transcription initiation site revealed that nm23-M2 mRNA starts with a terminal oligopyrimidine sequence, which is known to render mRNA translation dependent on mitogenic factors. Recently, the nm23-M2 locus was identified as a common leukemia retrovirus integration site, suggesting that it plays a role in leukemia development. The expression of Nm23 from a retroviral vector in the absence of its 5'-untranslated region caused constitutive polysome association of nm23-M2. Polysome-association and protein expression of endogenous nm23-M2 declined during differentiation of erythroid progenitors, suggesting a role for Nm23-M2 in progenitor expansion. Taken together, nm23-m2 exemplifies that cytokine-dependent control of translation initiation is an important mechanism of gene expression regulation.
GBA variants influence cognitive status in amyotrophic lateral sclerosis (2021)

Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive degenerative disease of upper and lower motor neurons. Approximately 15% of patients display clinical features consistent with frontotemporal dementia (FTD) and 35% display milder degrees of cognitive and behavioural impairment at some stage during their illness.1 Several genes have been reported to cause both ALS and FTD. Nevertheless, it remains unclear why some patients with ALS develop cognitive impairment, while other cases, often within the same family, remain unaffected.

The GBA gene (OMIM *606463) encodes glucocerebrosidase (GCase), a lysosomal enzyme that converts glucocerebroside into glucose and ceramide. Heterozygous GBA mutations increase the risk of Parkinson’s disease (PD) and the risk of cognitive impairment in patients with PD.2

It is increasingly recognised that variants in genes causing Mendelian neurodegenerative diseases may exhibit pleiotropic effects and impact the phenotypic heterogeneity of those disorders. Moreover, lysosomal dysfunction has recently been associated with both Dementia with Lewy Bodies and FTD spectrum (online supplemental table 1). Based on this, we postulated that GBA variants may influence the cognitive status of patients with ALS.

### Supplementary data

[jnnp-2021-327426supp001.pdf]

We examined the GBA variants’ association with the risk of cognitive impairment in 751 patients with ALS from the population-based Piemonte and Valle d’Aosta Register for ALS that had undergone both a detailed neuropsychological evaluation and a whole-genome sequencing screening.3 Patients were classified as ALS with normal cognitive function (ALS-CN), ALS-FTD and ALS with intermediate cognitive deficits. The characteristics of the study population and a detailed description of neuropsychological testing and genetic screening are reported in online supplementarl materials in the Methods section.

A mutational screening of GBA exonic variants was performed and their frequencies were compared with an internal control cohort (see online supplemental methods, Subjects). To assess whether pathogenic rare variants (minor allele frequency<1%) in GBA contribute to …
Concept and requirements of a simulator for substation automation systems (2010)

Increase of dispersed generation in medium-voltage-grids and lack of practical experience with new standards form dangerous impacts on current control- and protection functions that are part of substation automation systems. To overcome these problems a simulator proposed, that supports the development of new protection systems and provides practical training opportunities in terms of IEC 61850. Real secondary equipment forms a substation, while the subimposed process, the primary equipment of the substation and the ambient power system, is simulated with a real-time simulator. Amplifiers are coupled to the simulator and allow for the emulation of the secondary currents and voltages of instrument transformers at a maximum frequency of up to 20 kHz. Conclusively relevant fault scenarios including transients during earth faults can be simulated.
Selective Laser Sintering of Tissue Engineering Scaffolds Using Poly(L-Lactide) Microspheres (2007)

This paper reports a study on the modification of a commercial selective laser sintering (SLS) machine for the fabrication of tissue engineering scaffolds from small quantities of poly(L-lactide) (PLLA) microspheres. A miniature build platform was designed, fabricated and installed in the build cylinder of a Sinterstation 2000 system. Porous scaffolds in the form of rectangular prism, 12.7×12.7×25.4 mm3, with interconnected square and round channels were designed using SolidWorks. For initial trials, DuraFormTM polyamide powder was used to build scaffolds with a designed porosity of ~70%. The actual porosity was found to be ~83%, which indicated that the sintered regions were not fully dense. PLLA microspheres in the size range of 5-30 μm were made using an oil-in-water emulsion solvent evaporation procedure and they were suitable for the SLS process. A porous scaffold was sintered from the PLLA microspheres with a laser power of 15W and a part bed temperature of 60oC. SEM examination showed that the PLLA microspheres were partially melted to form the scaffold. This study has demonstrated that it is feasible to build tissue engineering scaffolds from small amounts of biomaterials using a commercial SLS machine with suitable modifications.
Modular event-based systems (2002)

Event-based systems are developed and used to integrate components in loosely coupled systems. Research and product development have focused so far on efficiency issues but neglected methodological support to build such systems. In this article, the modular design and implementation of an event system is presented which supports scopes and event mappings, two new and powerful structuring methods that facilitate engineering and coordination of components in event-based systems. We give a formal specification of scopes and event mappings within a trace-based formalism adapted from temporal logic. This is complemented by a comprehensive introduction to the event-based style, its benefits and requirements.
Excess noise factors for conventional and superlattice avalanche photodiodes and photomultiplier tubes (1986)

Light falling on a photodetector produces an output current that fluctuates. The noise in this signal arises from two sources: randomness in the photon arrivals and randomness in the carrier multiplication process intrinsic to the photodetector. A general formula is derived for the variance of the photodetector output current in terms of parameters characterizing these two sources of randomness (the photon-number variance-to-mean ratio for the light and the excess noise factor for the detector). An important special case of this formula illustrates that the output-current variance is directly proportional to the detector excess noise factor when the number of photons at the input to the detector is Poisson distributed. Explicit expressions for excess noise factors are provided for three kinds of photodetectors: the double-carrier conventional avalanche photodiode, the double-carrier superlattice avalanche photodiode, and the photomultiplier tube. The results for the double-carrier superlattice device are new; it is shown that even a small amount of residual hole ionization can lead to a large excess noise factor. Comparisons are drawn among the detectors in terms of their noise properties.
Duplication events and the evolution of segmental identity (2005)

Duplication of genes, genomes, or morphological structures (or some combination of these) has long been thought to facilitate evolutionary change. Here we focus on studies of the teleost fishes to consider the conceptual similarities in the evolutionary potential of these three different kinds of duplication events. We review recent data that have confirmed the occurrence of a whole-genome duplication event in the ray-finned fish lineage, and discuss whether this event may have fuelled the radiation of teleost fishes. We then consider the fates of individual duplicated genes, from both a theoretical and an experimental viewpoint, focusing on our studies of teleost Hox genes and their functions in patterning the segmented hindbrain. Finally, we consider the duplication of morphological structures, once again drawing on our experimental studies of the hindbrain, which have revealed that experimentally induced duplicated neurons can produce functionally redundant neural circuits. We posit that the availability of duplicated material, independent of its nature, can lead to functional redundancy, which in turn enables evolutionary change.