gebhart/patrepeval huggingface dataset:
The Rise of Julius Caesar (1957)

When Caesar was born, probably in 100 b.c. , it is doubtful whether anyone at Rome would have expected a son of this secondary branch of the patrician Iulii Caesares to rise to great eminence in the state. The family, to be sure, was very old; it was said to have come to Rome from Alba Longa when King Tullus Hostilius destroyed the city, and the Iulii kept the tradition alive by maintaining associations with Alba and the Alban gods. But, in spite of the family's antiquity, the nobility of the Iulii, to paraphrase Cicero on another patrician, was better known to men of letters and to historians than it was to the voters. It was not even very well known to men of letters and historians, for the ten or eleven lulii who reached high office in the fifth and fourth centuries hardly average a line apiece in the six books that Livy devotes to their period—books crowded with vivid stories of patrician families like the Fabii, the Manlii, and the Valerii.
Visual data fusion for applications of high-resolution numerical weather prediction (2000)

Non-traditional applications of scientific data challenge the typical approaches to visualization. In particular popular scientific visualization strategies fail when the expertise of the data consumer is in a different field than the one that generated the data and data from the user's domain must be utilized as well. This problem occurs when predictive weather simulations are used for a number of weather-sensitive applications. A data fusion approach is adopted for visualization design and utilized for specific example problems.
A tobacco plasma membrane calmodulin‐binding transporter confers Ni<sup>2+</sup> tolerance and Pb<sup>2+</sup> hypersensitivity in transgenic plants (1999)

All organisms require a minimal amount of metal ions to sustain their metabolism, growth and development. At the same time, their intrinsic metal-uptake systems render them vulnerable to toxic levels of metals in the biosphere. Using radiolabeled recombinant calmodulin as a probe to screen a tobacco cDNA library, we have discovered a protein designated NtCBP4 (Nicotiana tabacum calmodulin-binding protein) that can modulate plant tolerance to heavy metals. Structurally, NtCBP4 is similar to vertebrate and invertebrate K+ and to non-selective cation channels, as well as to recently reported proteins from barley and Arabidopsis. Here we report on the subcellular localization of NtCBP4 and the phenotype of transgenic plants overexpressing this protein. The localization of NtCBP4 in the plasma membrane was manifested by fractionating tobacco membranes on sucrose gradients or by aqueous two-phase partitioning, and subsequently using immunodetection. Several independent transgenic lines expressing NtCBP4 had higher than normal levels of NtCBP4. These transgenic lines were indistinguishable from wild type under normal growth conditions. However, they exhibited improved tolerance to Ni2+ and hypersensitivity to Pb2+, which are associated with reduced Ni2+ accumulation and enhanced Pb2+ accumulation, respectively. To our knowledge this is the first report of a plant protein that modulates plant tolerance or accumulation of Pb2+. We propose that NtCBP4 is involved in metal uptake across the plant plasma membrane. This gene may prove useful for implementing selective ion tolerance in crops and improving phytoremediation strategies.
Cellular targets and mechanisms of nitros(yl)ation: An insight into their nature and kinetics <i>in vivo</i> (2004)

There is mounting evidence that the established paradigm of nitric oxide (NO) biochemistry, from formation through NO synthases, over interaction with soluble guanylyl cyclase, to eventual disposal as nitrite/nitrate, represents only part of a richer chemistry through which NO elicits biological signaling. Additional pathways have been suggested that include interaction of NO-derived metabolites with thiols and metals to form S-nitrosothiols (RSNOs) and metal nitrosyls. Despite the overwhelming attention paid in this regard to RSNOs, little is known about the stability of these species, their significance outside the circulation, and whether other nitros(yl)ation products are of equal importance. We here show that N-nitrosation and heme-nitrosylation are indeed as ubiquitous as S-nitrosation in vivo and that the products of these reactions are constitutively present throughout the organ system. Our study further reveals that all NO-derived products are highly dynamic, have fairly short lifetimes, and are linked to tissue oxygenation and redox state. Experimental evidence further suggests that nitroso formation occurs substantially by means of oxidative nitrosylation rather than NO autoxidation, explaining why S-nitrosation can compete effectively with nitrosylation. Moreover, tissue nitrite can serve as a significant extravascular pool of NO during brief periods of hypoxia, and tissue nitrate/nitrite ratios can serve as indicators of the balance between local oxidative and nitrosative stress. These findings vastly expand our understanding of the fate of NO in vivo and provide a framework for further exploration of the significance of nitrosative events in redox sensing and signaling. The findings also raise the intriguing possibility that N-nitrosation is directly involved in the modulation of protein function.
Skin permeation of drugs - Diffusion and partitioning. (1985)

for gas-liquid contacting systems where explosive gases, volatile liquids and so on are used.
Bringing immunisation to the children of Deodurg (2002)

As the UK faces measles outbreaks and questions over MMR, Sally Mould reports on a immunisation project that has some surprising lessons
Boundary loss for highly unbalanced segmentation (2018)

Widely used loss functions for CNN segmentation, e.g., Dice or cross-entropy, are based on integrals over the segmentation regions. Unfortunately, for highly unbalanced segmentations, such regional summations have values that differ by several orders of magnitude across classes, which affects training performance and stability. We propose a boundary loss, which takes the form of a distance metric on the space of contours, not regions. This can mitigate the difficulties of highly unbalanced problems because it uses integrals over the interface between regions instead of unbalanced integrals over the regions. Furthermore, a boundary loss complements regional information. Inspired by graph-based optimization techniques for computing active-contour flows, we express a non-symmetric $L_2$ distance on the space of contours as a regional integral, which avoids completely local differential computations involving contour points. This yields a boundary loss expressed with the regional softmax probability outputs of the network, which can be easily combined with standard regional losses and implemented with any existing deep network architecture for N-D segmentation. We report comprehensive evaluations and comparisons on different unbalanced problems, showing that our boundary loss can yield significant increases in performances while improving training stability. Our code is publicly available: https://github.com/LIVIAETS/surface-loss .
Multi-beam photonic band gap structure (2003)

Photonic band gap structures with single and multiple defect sites are considered for application in multi-beam klystrons and particle accelerators. Coupling between the modes at defect sites and methods to damp unwanted higher order modes are evaluated. A conceptual design of a multi-beam PBG klystron is presented.
Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance. (1994)

The basal factor TFIIE is an important component of the RNA polymerase II transcription machinery. In our efforts to determine the role of TFIIE in the transcription process, we have begun to define the interactions between TFIIE and other basal transcription factors. Here we report that TFIIE binds selectively to the nonphosphorylated form of RNA polymerase II (IIa) and that this interaction is mediated by the 56-kD subunit of TFIIE. Additional binding studies reveal that TFII can interact with TBP as well as TFIID and that this interaction is mediated primarily via the 56-kD subunit. Our studies indicate that TFIIE also interacts with both subunits of TFIIF and with TFIIH, a multisubunit basal factor reported to catalyze RNA polymerase II CTD phosphorylation. Protein affinity assays demonstrate that TFIIE binds directly to ERCC-3, a DNA repair protein associated with TFIIH. More importantly, TFIIE affinity resin can selectively isolate transcriptionally competent TFIIH from a partially purified preparation and thereby may recruit TFIIH to the transcription complex in vivo. These multiple interactions between TFIIE, Pol II and TFIIH support a model in which TFIIE plays a role in promoter clearance as well as in the recruitment of proteins required for transcription-coupled DNA repair.
Sample-based forecasting exploiting hierarchical time series (2012)

Time series forecasting is challenging as sophisticated forecast models are computationally expensive to build. Recent research has addressed the integration of forecasting inside a DBMS. One main benefit is that models can be created once and then repeatedly used to answer forecast queries. Often forecast queries are submitted on higher aggregation levels, e. g., forecasts of sales over all locations. To answer such a forecast query, we have two possibilities. First, we can aggregate all base time series (sales in Austria, sales in Belgium...) and create only one model for the aggregate time series. Second, we can create models for all base time series and aggregate the base forecast values. The second possibility might lead to a higher accuracy but it is usually too expensive due to a high number of base time series. However, we actually do not need all base models to achieve a high accuracy, a sample of base models is enough. With this approach, we still achieve a better accuracy than an aggregate model, very similar to using all models, but we need less models to create and maintain in the database. We further improve this approach if new actual values of the base time series arrive at different points in time. With each new actual value we can refine the aggregate forecast and eventually converge towards the real actual value. Our experimental evaluation using several real-world data sets, shows a high accuracy of our approaches and a fast convergence towards the optimal value with increasing sample sizes and increasing number of actual values respectively.
Poxvirus vaccines for cancer and HIV therapy (2004)

The poxviridae have a long history of causing disease in society, and their biological effects in humans and other mammals have been extensively studied. In the 1980s, genetic engineering techniques were applied to vaccinia in order to create replicating recombinant vectors that could express inserted genes encoding influenza virus proteins. In animal models, these recombinant viruses were able to deliver their foreign antigens to the immune system and elicit a specific adaptive immune response. Since then, improvements in our understanding of immunobiology, as well as technical advances in bioengineering, have led to the creation and clinical testing of a large number of recombinant poxviruses as candidate vaccines. Poxviruses can infect a broad range of cells, replicate with high efficiency and elicit strong immune responses - factors that make them especially well-suited as vaccines for the prevention and treatment of human immunodeficiency virus (HIV) and cancer. Both of these diseases are characterised by chronic antigen expression in the setting of focal or global deficits in the immune system that hamper the generation of protective immunity. This review traces the history of poxviruses as pathogens and immunogens, examines some of the approaches that have been taken to design poxviral vaccines for HIV and cancer and summarises the results of existing clinical trials of these vectors. In addition, the review aims to identify some of the factors that may shape the development of future therapies based on recombinant poxviruses.
Spies Within Metal-Organic Frameworks: Investigating Metal Centers Using Solid-State NMR (2014)

Structural characterization of metal–organic frameworks (MOFs) is crucial, since an understanding of the relationship between the macroscopic properties of these industrially relevant materials and their molecular-level structures allows for the development of new applications and improvements in current performance. In many MOFs, the incorporated metal centers dictate the short- and long-range structure and porosity of the material. Here we demonstrate that solid-state NMR (SSNMR) spectroscopy targeting NMR-active metal centers at natural abundance, in concert with ab initio density functional theory (DFT) calculations and X-ray diffraction (XRD), is a powerful tool for elucidating the molecular-level structure of MOFs. 91Zr SSNMR experiments on MIL-140A are paired with DFT calculations and geometry optimizations in order to detect inaccuracies in the reported powder XRD crystal structure. 115In and 139La SSNMR experiments on sets of related MOFs at two different magnetic fields illustrate the sensitivity of the 115In/139La electric field gradient tensors to subtle differences in coordination, bond length distribution, and ligand geometry about the metal center. 47/49Ti SSNMR experiments reflect the presence or absence of guest solvent in MIL-125(Ti), and when combined with DFT calculations, these SSNMR experiments permit the study of local hydroxyl group configurations within the MOF channels. 67Zn SSNMR experiments and DFT calculations are also used to explore the geometry near Zn within a set of four MOFs as well as local disordering caused by distributions of different linkers around the metal. SSNMR spectroscopy of metal centers offers an impressive addition to the arsenal of techniques for MOF characterization and is particularly useful in cases where XRD information may be ambiguous, incomplete, or unavailable.
BCL-2 IMMUNOREACTIVITY INCREASES WITH SEVERITY OF CIN: A STUDY OF NORMAL CERVICAL EPITHELIA, CIN, AND CERVICAL CARCINOMA (1996)

The presence of the BCL-2 protein, a marker for inhibition of programmed cell death, was studied in a series of routinely processed cervical tissues, consisting of normal endocervical (n = 40) and ectocervical epithelium (n = 27), squamous metaplastic epithelium (n = 30), CIN (cervical intraepithelial neoplasia) lesions (n = 32), and cervical carcinomas (n = 13). BCL-2 was strongly expressed in the basal cell compartment of normal ectocervical squamous epithelium and in nearly all reserve cells, while in endocervical columnar cells it was moderately expressed. In immature squamous metaplastic epithelium, BCL-2 expression varied. Half of the cases showed only basal cell staining, while the other half showed staining also in suprabasal layers. BCL-2 could be detected in all premalignant lesions, showing a striking increase in the number of positive cells with increasing severity of CIN, in combination with a mild increase in staining intensity. All adenocarcinomas were positive (n = 5), while five of eight squamous cell carcinomas expressed BCL-2. Based on these results, it is hypothesized that both the larger number of cells staining with BCL-2 in higher grades of CIN and the increase in staining intensity imply an increasing protection of these neoplastic conditions against programmed cell death. This protection facilitates not only continuing proliferation, but also the induction of genetic instability in dysplastic epithelial cells; it may thus reflect the greater capacity of the more severe CIN lesions to evolve into cervical carcinoma.
Vitamin D Triggers Killing of Burkitt Lymphoma Cells by Human Macrophages (2012)

Abstract Abstract 1035 Introduction: Distinct macrophage subsets have been linked with either protective or pathogenic roles in cancer. M2 macrophages have been shown to suppress adaptive tumour-specific immune responses and promote tumour growth, while M1 macrophages eliminate neoplastic cells and activate tumour-killing mechanisms. Macrophages isolated from solid tumours (tumor-associated macrophages, TAM) reveal a suppressive and tumor promoting M2-like phenotype. However, it remains unclear which tumoricidal effector mechanisms are compromised in theses immune cells. While infilatration of macrophages is a characteristic morphological hallmark in Burkitts' lymphoma (BL), the phenotype and functional properties of TAM as part of the stroma are poorly understood. In this study we investigated the phenotype of lymphoma associated macrophages (LAM) and the mechanisms by which macrophages are able to modulate the growth of tumor cells. Methods: We included 19 patients diagnosed with BL and 20 patients with benign reactive lymphadenopathy as a control group. Phenotypic characterizations of LAM were evaluated by immunohistochemistry and by qPCR in paraffin embedded tissues. To investigate anti lymphoma cytotoxicity of distinct macrophage subsets we generated macrophages from PBMC either by GM-CSF to create the M1 phenotype, or by M-CSF to obtain the M2 phenotype. M1 and M2 macrophages were coincubated them with several BL cell lines and cytotoxicity was analyzed by flow cytometry, qPCR and immunofluorescence. Results: First, we could demonstrate that BL infiltrating macrophages displayed an anti-inflammatory M2-phenotype characterized by expression of surface markers such as CD68 and CD163. Second, we identified impaired vitamin D metabolism in LAM and M2 macrophages as demonstrated by low expression of vitamin D receptor and Cyp27B1, and increased expression of Cyp24A1. Third, macrophages revealed a reduced cytotoxic potential towards lymphoma cells which was dependent on the expression of the vitamin D dependent peptide cathelicidin. Finally, we could demonstrate that excess supplementation of calcitriol led to increased cytotoxicity of M1- and M2 macrophages towards BL cells. Conclusions: These results suggest a mechanism in which vitamin D is required for innate immunity to overcome the ability of lymphoma cells to evade macrophage-mediated antitumoral responses. The present findings underscore the importance of vitamin D for sustaining innate immunity and imply that the therapeutic activation of the vitamin D pathway may even result in triggering tumoricidal effector mechanisms of LAM. Disclosures: No relevant conflicts of interest to declare.
Reactions of azelaaldehydic esters (1969)

Abstract Alkyl azelaaldehydates and their acetals can undergo reactions at either the aldehyde or the ester group to form a variety of novel and reactive monomers and polymers. Pertinent reactions of the aldehyde group (and resultant products) include acetalization with pentaerythritol (diester‐acetal), acetalization with glycerol (hydroxy ester‐acetal), hydrogenation (hydroxy ester), reductive alkylation of ammonia (amino acid and imino diester), aldolization (dibasic acid) and hydrazone formation (azine dibasic acids). Reactions at the ester group include aminolysis (diacid amides) and hydrazinolysis (hydrazide acetal). These various products can undergo self‐condensation or condensation with glycols or diamines to form polyesters, polyamides, poly (ester‐acetals) and poly (amideacetals). Polymers with cyclic acetal structures in the polymer backbone have latent crosslinking capabilities.
Synthesis of SnO<sub>2</sub>‐ZnO Core‐Shell Nanowires and Their Optoelectronic Properties (2012)

Zinc oxides deposited on Tin dioxide nanowires have been successfully synthesized by atomic layer deposition (ALD). The diameter of SnO 2 ‐ZnO core‐shell nanowires is 100 nm by ALD 200 cycles. The result of electricity measurements shows that the resistance of SnO 2 ‐ZnO core‐shell nanowires (ALD: 200 cycles) is 925 Ω, which is much lower than pure SnO 2 nanowires (3.6 × 10 6 Ω). The result of UV light test shows that the recovery time of SnO 2 ‐ZnO core‐shell nanowires (ALD: 200 cycles) is 328 seconds, which is lower than pure SnO 2 nanowires (938 seconds). These results demonstrated that the SnO 2 ‐ZnO core‐shell nanowires have potential application as UV photodetectors with high photon‐sensing properties.
Cantilever-Type Microelectromechanical Systems Probe Card with Through-Wafer Interconnects for Fine Pitch and High-Speed Testing (2004)

A new microelectromechanical systems (MEMS) probe card made of electroplated nickel cantilevers, which has compliant structure, with through-wafer interconnections for IC testing is developed. The measured contact resistance was less than 0.5 ohm and leakage current was approximately 0.13 nA between tips and pads. In addition, planarity of tips and the alignment of x - and y -axes were satisfied with conventional needle probe card performance. Therefore, this probe card is suitable for wafer-level burn-in testing and function testing of memory and RF devices. In particular, since through-wafer interconnection can offer the shortest signal line path and reduce signal delay, it is possible to implement fine pitch and high-speed devices. The probe was fabricated with the 4-inch silicon substrate.
The physics and the chemistry of the heat pad (2008)

Flexing a metallic disk triggers the crystallization of the supercooled sodium acetate solution contained in commercial heat pads. Many mechanisms have been proposed to explain the apparent nucleation of crystalline material. In this paper a simple experiment is described that demonstrates that nucleation is triggered by preserving seed crystals clamped between opposing metal surfaces. An explanation for the retention of the crystalline particles is the elevated melting point caused by very high local pressures. A series of thermophysical properties of the sodium acetate solution is also measured, including the available enthalpy upon crystallization of the supercooled substance, and liquid and solid phase specific heat capacities.
Improved Protocols for the Synthesis and Halogenation of Sterically Hindered Metalloporphyrins (1996)

Improved procedures are described for the synthesis of meso-tetrakis(2,6-dichlorophenyl)porphyrin and for subsequent perhalogenation of the porphyrin ring.
Biomimetic Nanofibrous Scaffolds:  Preparation and Characterization of PGA/Chitin Blend Nanofibers (2006)

Electrospinning of poly(glycolic acid) (PGA)/chitin blend solutions in 1,1,1,3,3,3-hexafluoro-2-propanol was investigated to fabricate biodegradable and biomimetic nanostructured scaffolds for tissue engineering. The morphology of the electrospun PGA/chitin blend nanofibers was investigated with a field emission scanning electron microscope. The PGA/chitin blend fibers have average diameters of around 140 nm, and their diameters have a distribution in the range 50-350 nm. The miscibility of PGA/chitin blend fibers was examined by differential scanning calorimetry. The PGA and chitin were immiscible in the as-spun nanofibrous structure. An in vitro degradation study of PGA/chitin blend nanofibers was conducted in phosphate-buffered saline, pH 7.2. It was found that the hydrolytic cleavage of PGA in the blend nanofibers was accelerated by the coexistence of hydrophilic chitin. To assay the cytocompatability and cell behavior on the PGA/chitin blend nanofibrous scaffolds, cell attachment and spreading of normal human epidermal fibroblasts seeded on the scaffolds were studied. Our results indicate that the PGA/chitin blend nanofibrous matrix, particularly the one that contained 25% PGA and 75% chitin with bovine serum albumin coating, could be a good candidate for tissue engineering scaffolds, because it has an excellent cell attachment and spreading for normal human fibroblasts.