gebhart/patrepeval huggingface dataset:
Longitudinal and transverse modulation of electron wave function with light, and its application to electron microscopy (2021)

Conventional electron microscopy operates with flat electron wave fronts. Employing attenuative or electrostatic phase plates allows transversally modulating the wave front, enhancing cross-sections of particular scattering channels. Utilization of light from coherent ultrafast sources allows modulating electrons phase both transversally and longitudinally. This results in a plethora of phenomena, as well as conceptually new techniques such as non-local electron holography of light fields and generation of ultrafast electron vortex beams, which we present in this contribution.
ChemInform Abstract: SYNTHESIS OF THE TAXANE RING SYSTEM (1985)

Abstract Die Synthese der Verbindungen (V) und (VI) mit Taxanringsystem wird beschrieben.
An Alloantibody Recognizing the FVIII A1 Domain in a Patient with CRM Reduced Haemophilia A due to Deletion of a Large Portion of the A1 Domain DNA Sequence (2000)

Summary We report the development of a FVIII inhibitor in a patient with severe, cross reacting material reduced (CRMR) haemophilia A. The level of Factor VIII antigen (FVIII:Ag) measured by ELISA using anti- C2 monoclonal and alloantibodies was 1.9 U/dl. This baseline FVIII:Ag level was increased to 8.3 U/dl after administration of DDAVP. The anti-FVIII inhibitor titer was 2.9 Bethesda U/ml. DNA analysis showed a large deletion of the FVIII gene from exon 4 to 7, corresponding to amino acid residues 111-317 included within the A1 domain. The size of the gene deletion was approximately 28 kb. 5' and 3' breakpoints were identified by sequencing in intron 3 and intron 7, respectively. FVIII mRNA was detected in the patient’s peripheral lymphocytes and the deletion spanning exon 4 to 7 was confirmed at the RNA level. Immunoprecipitation experiments using 125I labeled A1, A2 and light chain demonstrated that the inhibitor reacted only with the 54 kDa A1 domain. The inhibitor activity was more than 95% neutralized by A1 domain polypeptide. Our findings suggest a close relationship between the inhibitor epitope and the specific gene deletion with regard to the pathogenesis of the inhibitor in this patient.
Hypothesis: Kisspeptin Mediates Male Hypogonadism in Obesity and Type 2 Diabetes (2010)

Hypogonadism occurs commonly in men with type 2 diabetes (T2DM) and severe obesity. Current evidence points to a decreased secretion of gonadotropin-releasing hormone (GnRH) from the hypothalamus and thereby decreased secretion of gonadotropins from the pituitary gland as a central feature of the pathophysiology in these men. Hyperglycaemia, inflammation, leptin and oestrogen-related feedback have been proposed to make aetiological contributions to the hypogonadotropic hypogonadism of T2DM. However, the neuroendocrine signals that link these factors with modulation of GnRH neurons have yet to be identified. Kisspeptins play a central role in the modulation of GnRH secretion and, thus, downstream regulation of gonadotropins and testosterone secretion in men. Inactivating mutations of the kisspeptin receptor have been shown to cause hypogonadotropic hypogonadism in man, whilst an activating mutation is associated with precocious puberty. Data from studies in experimental animals link kisspeptin expression with individual factors known to regulate GnRH secretion, including hyperglycaemia, inflammation, leptin and oestrogen. We therefore hypothesise that decreased endogenous kisspeptin secretion is the common central pathway that links metabolic and endocrine factors in the pathology of testosterone deficiency seen in men with obesity and T2DM. We propose that the kisspeptin system plays a central role in integrating a range of metabolic inputs, thus constituting the link between energy status with the hypothalamic-pituitary-gonadal axis, and put forward potential clinical studies to test the hypothesis.
Adhesion test standardization for multichip module packages (2002)

This paper summarizes the adhesion test standard and technique developed collectively by groups from the IBM Research Division, Yorktown Heights, and the Development Laboratory of IBM Microelectronics Division at East Fishkill. This activity was Initiated since the increased complexity of interconnection technologies require a large number of interfaces to maintain their integrity while being subjected to a large variety of processes. For example, reliable adhesion of polymer layers to metals and ceramics plays a vital role in several IBM key product technologies, such as the recently announced Glass-Ceramic Module multichip packaging technology used in the system 390/ES9000, models 820, 900 and 9021, computers and the Metallized Ceramic Polyimide (MCP) products. During the course of these product development cycles, it was noted that, sample preparation and measurement techniques can strongly affect the measured adhesion strength of a multi-component structure such as that found in multichip and multilayer modules. As a result of the observed variability in a multitude of adhesion measurements from many IBM laboratories, it was decided that standardization of the sample preparation and adhesion measurement techniques was required. During the course of collective work between a large number of participants, it became clear, that once a certain number of rules are followed, data collected from different workers can be compared. These rules form the basis of the peel standard which is discussed here. Once the standard measurement of adhesion is implemented, various adhesion promotion techniques can be directly compared, which lead to a swift and facile improvement in the reliability of products and in their development cycle time.
Emerging multidisciplinary research across database management systems (2011)

The database community is exploring more and more multidisciplinary avenues: Data semantics overlaps with ontology management; reasoning tasks venture into the domain of artificial intelligence; and data stream management and information retrieval shake hands, e.g., when processing Web click-streams. These new research avenues become evident, for example, in the topics that doctoral students choose for their dissertations. This paper surveys the emerging multidisciplinary research by doctoral students in database systems and related areas. It is based on the PIKM 2010, which is the 3rd Ph.D. workshop at the International Conference on Information and Knowledge Management (CIKM). The topics addressed include ontology development, data streams, natural language processing, medical databases, green energy, cloud computing, and exploratory search. In addition to core ideas from the workshop, we list some open research questions in these multidisciplinary areas.
TGF-β-dependent Lymphoid Tissue Residency of Stem-like T cells Limits the Response to Tumor Vaccine (2021)

Abstract Stem-like CD8 + T cells represent the key subset responding to multiple tumor immunotherapies, including tumor vaccination. However, the signals that control the differentiation of stem-like T cells are not entirely known. Most previous investigations on stem-like T cells are focused on tumor infiltrating T cells (TIL). The behavior of stem-like T cells in other tissues remains to be elucidated. Tissue-resident memory T cells (T RM ) are often defined as a non-circulating T cell population residing in non-lymphoid tissues. TILs carrying T RM features are associated with better tumor control. Here, we found that stem-like CD8 + T cells differentiated into T RM s in a TGF-β and tumor antigen dependent manner almost exclusively in tumor draining lymph node (TDLN). TDLN-resident stemlike T cells were negatively associated with the response to tumor vaccine. In other words, after tumor vaccine, TDLN stem-like T cells transiently lost T RM features, differentiated into migratory effectors and exerted tumor control.
Cover Picture: Enhanced Operational Stability of the Up‐Conversion Fluorescence in Films of Palladium–Porphyrin End‐Capped Poly(pentaphenylene) (ChemPhysChem 7/2005) (2005)

The cover picture shows poly(laddertype pentaphenylene) hosts end‐capped with palladium tetratolylporphyrin guest moieties. After absorption of photons (green arrows) in the singlet Q‐band of the porphyrin molecule, due to effective intersystem crossing, the porphyrin's long‐lived triplet state is populated. In their Communication on page 1250 Baluschev et al. consider the excited triplet states as a reservoir of excited states for the subsequent energy transfer (grey arrows) leading to up‐conversion photoluminescence (blue arrow) of the host molecules. Phosphorescence emission of the guest molecules is also observed (red arrow).
Abstract 479: Modeling miRNA induced silencing in breast cancer with PARADIGM (2017)

Abstract Introduction: MicroRNAs play an important role in regulation of gene expression and are known biomarkers for breast cancer as well as other malignancies. PARADIGM is a pathway based algorithm that allows for integration of multiple genomic data types with a curated pathway database to make pathway activity predictions. We added a model of gene silencing due to miRNA to the PARADIGM algorithm in order to study miRNA expression in a pathway context. Results: We curated a set of 7751 miRNA-mRNA interactions from the intersection of 3 target prediction algorithms. These interactions involved 66 miRNA and 2814 mRNA transcripts. We ran this model on global DNA copy number, RNAseq and miRNAseq data from 697 patients in the TCGA breast cancer cohort, and studied changes in the interactions between miRNAs and their targets between different tumor subtypes. The median activity of the RNA-induced silencing complex (RISC) predicted by our model is significantly higher in Basal tumors than other subtypes. In addition, RISC activity is significantly associated with overall survival of patients with Luminal A tumors. The miRNA-target pairs with the largest correlation changes between Basal and Luminal A subtypes were enriched for putative oncogenes and oncomirs. The mRNA targets are involved in a number of important signaling pathways including PI3K-AKT, JAK-STAT, and Ras. Many of these highly differential links involved the miR-16 family of miRNAs which are known tumor suppressors. miR-16 shows significantly lower activity in basal tumors than other subtypes. Conclusions: By looking at changes in miRNA-target links between tumor subtypes, our algorithm was able to identify both miRNAs and target genes involved in pathways relevant to breast cancer. Our predictions of overall RNA-induced silencing activity show prognostic value in both determining subtype and predicting overall survival within subtypes. Citation Format: Andrew J. Sedgewick, Panayiotis V. Benos, Shahrooz Rabizadeh, Patrick Soon-Shiong, Charles J. Vaske. Modeling miRNA induced silencing in breast cancer with PARADIGM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 479. doi:10.1158/1538-7445.AM2017-479
Supplementary Figure 1 from STAT3 Inhibition Enhances the Therapeutic Efficacy of Immunogenic Chemotherapy by Stimulating Type 1 Interferon Production by Cancer Cells (2023)

&lt;p&gt;Supplementary Figure 1. Effect of DOXO on STAT3 phosphorylation.&lt;/p&gt;
Identification and Characterization of a High-Affinity Interaction Between v-Crk and Tyrosine-Phosphorylated Paxillin in CT10-Transformed Fibroblasts (1993)

The genome of avian sarcoma virus CT10 encodes a fusion protein in which viral Gag sequences are fused to cellular Crk sequences containing primarily Src homology 2 (SH2) and Src homology 3 (SH3) domains. Transformation of chicken embryo fibroblasts (CEF) with the Gag-Crk fusion protein results in the elevation of tyrosine phosphorylation on specific cellular proteins with molecular weights of 130,000, 110,000, and 70,000 (p130, p110, and p70, respectively), an event which has been correlated with cell transformation. In this study, we have identified the 70-kDa tyrosine-phosphorylated protein in CT10-transformed CEF (CT10-CEF) as paxillin, a cytoskeletal protein suggested to be important for organizing the focal adhesion. Tyrosine-phosphorylated paxillin was found to be complexed with v-Crk in vivo as evident from coimmunoprecipitation studies. Moreover, a bacterially expressed recombinant glutathione S-transferase (GST)-CrkSH2 fragment bound paxillin in vitro with a subnanomolar affinity, suggesting that the SH2 domain of v-Crk is sufficient for binding. Mapping of the sequence specificity of a GST-CrkSH2 fusion protein with a partially degenerate phosphopeptide library determined a motif consisting of pYDXP, and in competitive coprecipitation studies, an acetylated A(p)YDAPA hexapeptide was able to quantitatively inhibit the binding of GST-CrkSH2 to paxillin and p130, suggesting that it meets the minimal structural requirements necessary for the interaction of CrkSH2 with physiological targets. To investigate the mechanism by which v-Crk elevates the tyrosine phosphorylation of paxillin in vivo, we have treated normal CEF and CT10-CEF with sodium vanadate to inhibit protein tyrosine phosphatase activity. These data suggest that paxillin is involved in a highly dynamic kinase-phosphatase interplay in normal CEF and that v-Crk binding may interrupt this balance to increase the steady-state level of tyrosine phosphorylation. By contrast, the 130-kDa protein was not tyrosine phosphorylated upon vanadate treatment of normal CEF and only weakly affected in the CT10-CEF, suggesting that a different mechanism may be involved in its phosphorylation.
The design of an SRAM-based field-programmable gate array. I. Architecture (1999)

Field-programmable gate arrays (FPGAs) are now widely used for the implementation of digital systems, and many commercial architectures are available. Although the literature and data books contain detailed descriptions of these architectures, there is very little information on how the high-level architecture was chosen, and no information on the circuit-level or physical design of the devices. This paper describes the high-level architectural design of a static-random-access memory programmable FPGA. A forthcoming Part II will address the circuit design issues through to the physical layout. The logic block and routing architecture of the FPGA was determined through experimentation with benchmark circuits and custom-built computer-aided design tools. The resulting logic block is an asymmetric tree of four-input lookup tables that are hard-wired together and a segmented routing architecture with a carefully chosen segment length distribution.
A Short and Efficient Synthesis of (2S,3S,4S)-tert-Butyl 3,4-Dihydroxy-2-(methoxymethyl)-5-oxopyrrolidine-1-carboxylate (2010)

Asymmetric synthesis of the title compound was accomplished starting from L-serine. Stannoxane-mediated lactamization provided the key intermediate in good yield.
Reducing the Modem Complexity and Achieving Deep Coverage in LTE for Machine-Type Communications (2016)

The Internet of Things (IoT) has emerged as one of the focal points in the evolution of cellular networks, and has motivated the introduction of several features that facilitate Machine-Type Communications (MTC) in LTE networks. These features serve the MTC goals of reduced User Equipment (UE) modem cost and complexity, Coverage Enhancement (CE) to support UEs in remote radio locations, and an improved battery lifetime. In this paper, we discuss the features specified in LTE Release 12 and Release 13 for reducing the UE modem cost up to 81% compared to the least expensive broadband LTE UE modem. Further, we describe the techniques specified in Release 13 for the CE of physical channels that carry data or control information. We provide link-level simulation results for the CE performance over various physical channels in terms of their error rates and per-user throughput.
Cell Surface Presenilin-1 Participates in the γ-Secretase-like Proteolysis of Notch (1999)

Presenilin-1 (PS1), a polytopic membrane protein primarily localized to the endoplasmic reticulum, is required for efficient proteolysis of both Notch and beta-amyloid precursor protein (APP) within their trans- membrane domains. The activity that cleaves APP (called gamma-secretase) has properties of an aspartyl protease, and mutation of either of the two aspartate residues located in adjacent transmembrane domains of PS1 inhibits gamma-secretase processing of APP. We show here that these aspartates are required for Notch processing, since mutation of these residues prevents PS1 from inducing the gamma-secretase-like proteolysis of a Notch1 derivative. Thus PS1 might function in Notch cleavage as an aspartyl protease or di-aspartyl protease cofactor. However, the ER localization of PS1 is inconsistent with that hypothesis, since Notch cleavage occurs near the cell surface. Using pulse-chase and biotinylation assays, we provide evidence that PS1 binds Notch in the ER/Golgi and is then co-transported to the plasma membrane as a complex. PS1 aspartate mutants were indistinguishable from wild-type PS1 in their ability to bind Notch or traffic with it to the cell surface, and did not alter the secretion of Notch. Thus, PS1 appears to function specifically in Notch proteolysis near the plasma membrane as an aspartyl protease or cofactor.
Mechanisms of macular edema: Beyond the surface (2017)

Macular edema consists of intra- or subretinal fluid accumulation in the macular region. It occurs during the course of numerous retinal disorders and can cause severe impairment of central vision. Major causes of macular edema include diabetes, branch and central retinal vein occlusion, choroidal neovascularization, posterior uveitis, postoperative inflammation and central serous chorioretinopathy. The healthy retina is maintained in a relatively dehydrated, transparent state compatible with optimal light transmission by multiple active and passive systems. Fluid accumulation results from an imbalance between processes governing fluid entry and exit, and is driven by Starling equation when inner or outer blood-retinal barriers are disrupted. The multiple and intricate mechanisms involved in retinal hydro-ionic homeostasis, their molecular and cellular basis, and how their deregulation lead to retinal edema, are addressed in this review. Analyzing the distribution of junction proteins and water channels in the human macula, several hypotheses are raised to explain why edema forms specifically in the macular region. "Pure" clinical phenotypes of macular edema, that result presumably from a single causative mechanism, are detailed. Finally, diabetic macular edema is investigated, as a complex multifactorial pathogenic example. This comprehensive review on the current understanding of macular edema and its mechanisms opens perspectives to identify new preventive and therapeutic strategies for this sight-threatening condition.
Hyperbaric spinal anesthesia with ropivacaine coadministered with sufentanil for cesarean delivery: a dose-response study. (2015)

Adjuvant sufentanil could achieve effective spinal anesthesia with low dose of hyperbaric ropivacaine for cesarean delivery. Two previous studies had calculated the 50% effective dose (ED50) of intrathecal ropivacaine coadministered with sufentanil for cesarean delivery. However, the 95% effective dose (ED95) of intrathecal hyperbaric ropivacaine coadministered with sufentanil for cesarean delivery remains uncertain. This study determined the ED95 of intrathecal hyperbaric ropivacaine coadministered with sufentanil for cesarean delivery. 80 ASA physical status I or II parturients undergoing elective cesarean delivery were enrolled in this prospective, randomized, double-blind investigation. A combined spinal and epidural anesthesia was performed at the L3-L4 interspace. Patients received a dose of spinal ropivacaine coadministered with sufentanil 5 μg diluted to 3.0 ml with normal saline and 0.5 ml of 10% dextrose: 7.5 mg (n = 20), 9.0 mg (n = 20), 10.5 mg (n = 20), or 12 mg (n = 20). An effective dose was defined as a dose that provided bilateral sensory block to T7 within 10 min after intrathecal drug administration and required no epidural top-up for surgery to be completed. The ED50 and ED95 values for successful anesthesia were determined using a logistic regression model. The ED50 (95% confidence interval [CI]) for successful anesthesia was 8.4 (4.0-9.8) mg and the ED95 (95% CI) was 11.4 (9.7-13.9) mg. The results show that the ED95 of intrathecal hyperbaric ropivacaine coadministered with sufentanil 5 μg for cesarean delivery was 11.4 mg. The addition of sufentanil could significantly reduce the dosage of ropivacaine.
Low-Energy Path to Dense HfO2 Thin Films with Aqueous Precursor (2011)

New, stable aqueous solutions have been developed for the deposition of high-quality HfO2 thin films. The low ionic strength of the solution relative to a stoichiometric salt provides the means to directly spin coat a film without organic additives. Peroxide mediates particle interaction in the solution, while enabling relatively low-energy pathways for condensation of the precursor species to a film. Film structure, chemistry, and density are investigated by X-ray diffraction, FT-IR, electron-probe microanalysis, SEM, and X-ray reflectivity. Results from these measurements collectively reveal that smooth and dense HfO2 films are readily produced from the precursors with annealing at moderate temperatures. Optical properties of the films are studied by spectroscopic ellipsometry and transmission/reflection measurements. The observed refractive indices (1.89−1.93) are comparable to those achieved via vapor deposition techniques. Dielectric properties are evaluated through integration of the films into capacitors and thin film transistors. Performance as capacitor dielectrics is characterized by leakage current densities <10 nA/cm2 (at 1 MV/cm) and breakdown fields up to 5.5 MV/cm. As gate dielectrics in thin film transistors with amorphous indium gallium zinc oxide channels, the films exhibit small gate leakage, enabling transistor performance with incremental mobilities near 13 cm2/V·s.
Fluorescence Interferometry (2008)

The use of fluorescence radiation is of fundamental importance for tackling measurement problems in the life sciences, with recent demonstrations of probing biological systems at the nanoscale. Usually, fluorescent light–based tools and techniques use the intensity of light waves, which is easily measured by detectors. However, the phase of a fluorescence wave contains subtle, but no less important, information about the wave; yet, it has been largely unexplored. Here, we introduce the concept of fluorescence interferometry to allow the measurement of phase information of fluorescent light waves. In principle, fluorescence interferometry can be considered a unique form of optical low‐coherence interferometry that uses fluorophores as a light source of low temporal coherence. Fluorescence interferometry opens up new avenues for developing new fluorescent light–based imaging, sensing, ranging, and profiling methods that to some extent resemble interferometric techniques based on white light sources. We propose two experimental realizations of fluorescence interferometry that detect the interference pattern cast by the fluorescence fields. This article discusses their measurement capabilities and limitations and compares them with those offered by optical low‐coherence interferometric schemes. We also describe applications of fluorescence interferometry to imaging, ranging, and profiling tasks and present experimental evidences of wide‐field cross‐sectional imaging with high resolution and large range of depth, as well as quantitative profiling with nanometer‐level precision. Finally, we point out future research directions in fluorescence interferometry, such as fluorescence tomography of whole organisms and the extension to molecular interferometry by means of quantum dots and bioluminescence.