gebhart/patrepeval huggingface dataset:
Solid Phase Synthesis of Oxytocin Analogues Conjugated to Polyamino Polycarboxylic Ligands (2009)

An easy solid phase synthesis of oxytocin analogues conjugated to polyaminopolycarboxylic ligand, such as diethylenetriaminepentaacetic acid (DTPA) and tetraazacyclododecanetetraacetic acid (DOTA) is reported. These new products can be labeled with suitable radiometals (e.g. 90Y, 111In, 177Lu), giving rise to radiopharmaceuticals with potential application in imaging and/or therapy of tumors over-expressing oxytocin receptors. Keywords: Oxytocin, solid phase peptide synthesis, targeting, DOTA, DTPA, radiolabeled peptides
Logical structure analysis of document images based on emergent computation (1999)

A new method for logical structure analysis of document images is proposed in this paper as the basis for a document reader which can extract logical information from various printed documents. The proposed system consists of five basic modules: typography analysis, object recognition, object segmentation, object grouping and object modification. Emergent computation, which is a key concept of artificial life, is adopted for the cooperative interaction among the modules in the system in order to achieve an effective and flexible behavior of the whole system. It has two principal advantages over other methods: adaptive system configuration for various and complex logical structures, and robust document analysis that is tolerant of erroneous feature detection.
Excited State Bilayer Quantum Dot Lasers at 1.3 µm (2011)

We report the realization of excited state bilayer quantum dot (QD) lasers in the 1.31 µm region. The higher saturated gain and lower scattering time of the excited states of the ensemble of QDs offers the opportunity for high modulation bandwidths. Gain measurements for these structures are discussed and compared to conventional QD laser structures. The extension of QD ground state operating wavelengths to 1.45 µm spanning the O- and E-band is also demonstrated.
Optimisation of large-radius jet reconstruction for the ATLAS detector in 13 TeV proton–proton collisions (2021)

Abstract Jet substructure has provided new opportunities for searches and measurements at the LHC, and has seen continuous development since the optimization of the large-radius jet definition used by ATLAS was performed during Run 1. A range of new inputs to jet reconstruction, pile-up mitigation techniques and jet grooming algorithms motivate an optimisation of large-radius jet reconstruction for ATLAS. In this paper, this optimisation procedure is presented, and the performance of a wide range of large-radius jet definitions is compared. The relative performance of these jet definitions is assessed using metrics such as their pileup stability, ability to identify hadronically decaying W bosons and top quarks with large transverse momenta. A new type of jet input object, called a ‘unified flow object’ is introduced which combines calorimeter- and inner-detector-based signals in order to achieve optimal performance across a wide kinematic range. Large-radius jet definitions are identified which significantly improve on the current ATLAS baseline definition, and their modelling is studied using pp collisions recorded by the ATLAS detector at $$\sqrt{s}=13~\text {TeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>13</mml:mn> <mml:mspace/> <mml:mtext>TeV</mml:mtext> </mml:mrow> </mml:math> during 2017.
VSTM2A Overexpression Is a Sensitive and Specific Biomarker for Mucinous Tubular and Spindle Cell Carcinoma (MTSCC) of the Kidney (2018)

Our recent study revealed recurrent chromosomal losses and somatic mutations of genes in the Hippo pathway in mucinous tubular and spindle cell carcinoma (MTSCC). Here, we performed an integrative analysis of 907 renal cell carcinoma (RCC) samples (combined from The Cancer Genome Atlas and in-house studies) and the Knepper data set of microdissected rat nephrons. We identified VSTM2A and IRX5 as novel cancer-specific and lineage-specific biomarkers in MTSCC. We then assessed their expression by RNA in situ hybridization (ISH) in 113 tumors, including 33 MTSCC, 40 type 1 papillary RCC, 8 type 2 papillary RCC, 2 unclassified RCC, 15 clear cell RCC, and 15 chromophobe RCC. Sensitivity and specificity were calculated as the area under the receiver operating characteristics curve (AUC). All MTSCC tumors demonstrated moderate to high expression of VSTM2A (mean ISH score=255). VSTM2A gene expression assessed by RNA sequencing strongly correlated with VSTM2A ISH score (r(2)=0.81, P=0.00016). The majority of non-MTSCC tumors demonstrated negative or low expression of VSTM2A. IRX5, nominated as a lineage-specific biomarker, showed moderate to high expression in MTSCC tumors (mean ISH score=140). IRX5 gene expression assessed by RNA sequencing strongly correlated with IRX5 ISH score (r(2)=0.69, P=0.00291). VSTM2A (AUC: 99.2%) demonstrated better diagnostic efficacy than IRX5 (AUC: 87.5%), and may thus serve as a potential diagnostic marker to distinguish tumors with overlapping histology. Furthermore, our results suggest MTSCC displays an overlapping phenotypic expression pattern with the loop of Henle region of normal nephrons.
Development and analytical performance of a new ARCHITECT automated dipeptidyl peptidase-4 immunoassay (2017)

These analyses indicate that the ARCHITECT DPP-4 Immunoassay is a reliable and robust method for measuring serum DPP-4 concentration.
Towards Zero-Shot Frame Semantic Parsing for Domain Scaling (2017)

State-of-the-art slot filling models for goal-oriented human/machine conversational language understanding systems rely on deep learning methods. While multi-task training of such models alleviates the need for large in-domain annotated datasets, bootstrapping a semantic parsing model for a new domain using only the semantic frame, such as the back-end API or knowledge graph schema, is still one of the holy grail tasks of language understanding for dialogue systems. This paper proposes a deep learning based approach that can utilize only the slot description in context without the need for any labeled or unlabeled in-domain examples, to quickly bootstrap a new domain. The main idea of this paper is to leverage the encoding of the slot names and descriptions within a multi-task deep learned slot filling model, to implicitly align slots across domains. The proposed approach is promising for solving the domain scaling problem and eliminating the need for any manually annotated data or explicit schema alignment. Furthermore, our experiments on multiple domains show that this approach results in significantly better slot-filling performance when compared to using only in-domain data, especially in the low data regime.
Adaptive microphone array employing calibration signals: an analytical evaluation (1999)

This paper gives an analytical description of an adaptive microphone array that facilitates a simple built-in calibration to the environment and instrumentation. This method, suggested for use in hands-free mobile telephones and speech recognition systems for cars, provides speech enhancement and acoustic echo-cancellation. The scheme offers several advantages, such as a simple calibration procedure, suppression of directional sources, versatile robust beamforming, and reduced target signal distortion. The analysis employs noncausal Wiener filters yielding compact and effective theoretical suppression limits.
Cellular uptake mechanisms and responses to NO transferred from mono- and poly-S-nitrosated human serum albumin (2011)

Endogenous S-nitrosated human serum albumin (E-Mono-SNO-HSA) is a large molecular weight nitric oxide (NO) carrier in human plasma, which has shown many beneficial effects in different animal models. To construct more efficient SNO-HSA preparations, SNO-HSA with many conjugated SNO groups has been prepared using chemical modification (CM-Poly-SNO-HSA). We have compared the properties of such a preparation to those of E-Mono-SNO-HSA. Cellular uptake of NO from E-Mono-SNO-HSA partly takes place via low molecular weight thiol, and it results in cytoprotective effects by induction of heme oxygenase-1. By contrast, transfer of NO from CM-Poly-SNO-HSA into the cells is faster and more pronounced. The influx mainly takes place by cell-surface protein disulfide isomerase. The considerable NO inflow results in apoptotic cell death by ROS induction and caspase-3 activation. Thus, increasing the number of SNO groups on HSA does not simply intensify the cellular responses to the product but can also result in very different effects.
Heavy Metal Ions in Normal Physiology, Toxic Stress, and Cytoprotection (2007)

As a group, heavy metals include both those essential for normal biological functioning (e.g., Cu and Zn), and nonessential metals (e.g., Cd, Hg, and Pb). Both essential and nonessential metals can be present at concentrations that disturb normal biological functions, and which evoke cellular stress responses. The cellular targets for metal toxicity include tissues of the kidney, liver, heart, and the immune response and nervous systems. Intriguingly, manipulations of specific metals, their reservoirs, and the cellular stress response can have therapeutic effects on certain diseases. In this minireview, we will consider both the biological responses to stressful levels of heavy metal cations, and experimental and clinical manipulations of these cations as a means to improve human health parameters.
SAM: Squeeze-and-Mimic Networks for Conditional Visual Driving Policy Learning (2019)

We describe a policy learning approach to map visual inputs to driving controls conditioned on turning command that leverages side tasks on semantics and object affordances via a learned representation trained for driving. To learn this representation, we train a squeeze network to drive using annotations for the side task as input. This representation encodes the driving-relevant information associated with the side task while ideally throwing out side task-relevant but driving-irrelevant nuisances. We then train a mimic network to drive using only images as input and use the squeeze network's latent representation to supervise the mimic network via a mimicking loss. Notably, we do not aim to achieve the side task nor to learn features for it; instead, we aim to learn, via the mimicking loss, a representation of the side task annotations directly useful for driving. We test our approach using the CARLA simulator. In addition, we introduce a more challenging but realistic evaluation protocol that considers a run that reaches the destination successful only if it does not violate common traffic rules. A video summarizing this work is available at https://youtu.be/ipKAMzmJpMs , and code is available at https://github.com/twsq/sam-driving .
Predominance of weakly cytotoxic, T-betLowEomesNeg CD8+ T-cells in human gastrointestinal mucosa: implications for HIV infection (2016)

The gastrointestinal mucosa is an important site of HIV acquisition, viral replication, and pathogenesis. Immune cells in mucosal tissues frequently differ in phenotype and function from their non-mucosal counterparts. Although perforin-mediated cytotoxicity as measured in blood is a recognized correlate of HIV immune control, its role in gastrointestinal tissues is unknown. We sought to elucidate the cytotoxic features of rectal mucosal CD8<sup>+</sup> T-cells in HIV infected and uninfected subjects. Perforin expression and lytic capacity were significantly reduced in rectal CD8<sup>+</sup> T-cells compared with their blood counterparts, regardless of HIV clinical status; granzyme B (GrzB) was reduced to a lesser extent. Mucosal perforin and GrzB expression were higher in participants not on antiretroviral therapy compared with those on therapy and controls. Reduction in perforin and GrzB was not explained by differences in memory/effector subsets. Expression of T-bet and Eomesodermin was significantly lower in gut CD8<sup>+</sup> T-cells compared with blood, and in vitro neutralization of TGF-β partially restored perforin expression in gut CD8<sup>+</sup> T-cells. These findings suggest that rectal CD8<sup>+</sup> T-cells are primarily non-cytotoxic, and phenotypically shaped by the tissue microenvironment. Further elucidation of rectal immune responses to HIV will inform the development of vaccines and immunotherapies targeted to mucosal tissues.
Biodistribution and Toxicity Studies of PRINT Hydrogel Nanoparticles in Mosquito Larvae and Cells (2015)

Mosquito-borne diseases continue to remain major threats to human and animal health and impediments to socioeconomic development. Increasing mosquito resistance to chemical insecticides is a great public health concern, and new strategies/technologies are necessary to develop the next-generation of vector control tools. We propose to develop a novel method for mosquito control that employs nanoparticles (NPs) as a platform for delivery of mosquitocidal dsRNA molecules to silence mosquito genes and cause vector lethality. Identifying optimal NP chemistry and morphology is imperative for efficient mosquitocide delivery. Toward this end, fluorescently labeled polyethylene glycol NPs of specific sizes, shapes (80 nm x 320 nm, 80 nm x 5000 nm, 200 nm x 200 nm, and 1000 nm x 1000 nm) and charges (negative and positive) were fabricated by Particle Replication in Non-Wetting Templates (PRINT) technology. Biodistribution, persistence, and toxicity of PRINT NPs were evaluated in vitro in mosquito cell culture and in vivo in Anopheles gambiae larvae following parenteral and oral challenge. Following parenteral challenge, the biodistribution of the positively and negatively charged NPs of each size and shape was similar; intense fluorescence was observed in thoracic and abdominal regions of the larval body. Positively charged NPs were more associated with the gastric caeca in the gastrointestinal tract. Negatively charged NPs persisted through metamorphosis and were observed in head, body and ovaries of adults. Following oral challenge, NPs were detected in the larval mid- and hindgut. Positively charged NPs were more efficiently internalized in vitro than negatively charged NPs. Positively charged NPs trafficked to the cytosol, but negatively charged NPs co-localized with lysosomes. Following in vitro and in vivo challenge, none of the NPs tested induced any cytotoxic effects.
Heuristic formulas to dimension buffers in a DSL access network carrying persistent TCP-controlled traffic (2005)

Persistent TCP flows, DSL access networks, buffer dimensioning. The capacity of the (DSL) access network keeps increasing, while at the same time there is a trend to support, on top of web browsing applications that spurred the initial popularity of the Internet, more and more applications (e.g. peer-to-peer, time-shifted TV) that require the transport of long-lived flows over such an access network. During the transport of these long-lived flows associated with these (non-timecritical) applications it is important that the last mile link is efficiently used and that each flow gets its fair share of the available capacity and this is what TCP, ideally suited for these non-time-critical applications, aims to do. We work under the assumption that the rest of the network and the upstream, which needs to transport the ACKs, are appropriately dimensioned and thus we concentrate on the downlink and its associated link buffer (in a DSL access network it is in the DSLAM) which has a crucial impact on the efficiency and the fairness of the transport in “last mile”. Studies show that persistent TCP flows have the greatest impact on buffer requirement (and not short-lived (web) flows). We show that both requirements can be fulfilled by choosing the buffer large enough (so that there is no packet loss). We develop a heuristic formula to calculate the required buffer size. Unfortunately, this buffer size may turn out to be too large to
Evaluation of Chitosan-Tripolyphosphate Nanoparticles as a p-shRNA Delivery Vector: Formulation, Optimization and Cellular Uptake Study (2013)

Polysaccharides (especially chitosan) have recently attracted much attention as gene therapy delivery vehicles for their unique properties such as biocompatibility, biodegradability, low toxicity, and controlled release. Nanoparticles have strong potential as a carrier of plasmid short hairpin RNA (p-shRNA). This study aimed to find the optimum conditions for obtaining Chitosan/triphosphate (TPP)/p-shRNA nanoparticles by the ionic gelation method, and investigating the cellular uptake of the optimized nanoparticles. After applying the central composite design of response surface methodology (RSM), the optimum conditions for preparation of nanoparticles with small size and high loading efficiency were: chitosan/TPP ratio = 10, pH = 5.5 and N/P ratio = 11. The resulting nanoparticles had an average size of 172.8 ± 7 nm and loading efficiency of 71.5 ± 5%. SEM images showed spherical and smooth nanoparticles. The nanoparticles complexed with p-shRNA and may protect it against nuclease digestion. Cytotoxicity studies with HeLa and PC3 human cancer cells demonstrated that chitosan/TPP nanoparticles had low toxicity. Cellular uptake studies using HeLa cells showed that the nanoparticles entered the cells (cellular uptake) and delivered DNA, probably due to their favorable Zeta potential (approximately +28 mV) and small size.
Nonlinear Nanoimaging of Ultrafast Coherent Dynamics of Graphene (2019)

Using femtosecond adiabatic plasmonic nanofocusing, we image graphene in broadband four-wave mixing, revealing spatial heterogeneity, 6 fs coherent dynamics, and a long range spatial nonlocality. © 2019 The Author(s)
Identification of Campath-1 (CD52) as Novel Drug Target in Neoplastic Stem Cells in 5q-Patients with MDS and AML (2014)

The cell surface target Campath-1 (CD52) is expressed on NSC in a group of patients with MDS and AML. CD52 is a novel prognostic NSC marker and a potential NSC target in a subset of patients with MDS and AML, which may have clinical implications and may explain clinical effects produced by alemtuzumab in these patients.
Scanned Probe-Based Chemical and Thermomechanical Property Mapping of Polymeric Materials Suitable for Electronic Applications (2011)

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.
Angle-limited cavities for silicon solar cells (2002)

A light-confining cavity to enhance the absorption of light of solar cells that achieves the light confinement by reduction of the escaping etendue, rather than that of the entry aperture area, is presented. Therefore, its entry aperture is large and no secondary is required. The cavity performance is theoretically studied and experimentally demonstrated, showing more than a one-and-a-half-point increase in efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prediction of the reflected spectra from chirped fibre Bragg gratings embedded within cracked crossply laminates (2006)

Matrix cracking damage is a generic type of damage that develops under load in the off-axis plies of laminated composites and is generally the precursor of more serious damage mechanisms, particularly delamination. Hence, it is important to identify and if possible locate this type of damage. Chirped fibre Bragg grating sensors have been embedded in a transparent glass fibre reinforced plastic crossply laminate and changes to the reflected spectra as a consequence of crack development have been studied. An approximately sinusoidal variation of the intensity of the reflected spectrum occurs at the position of the crack, enabling both crack development and crack position to be identified. A simulation of a reflected spectrum, incorporating a stress transfer model to predict the strains and an optical model to predict the reflected spectrum, is in reasonable agreement with the experimental results.
The GR at inflammatory crossroads (2012)

The Glucocorticoid Receptor (GR) is one of the most potent anti-inflammatory drug targets in clinical use today and one of the most powerful metabolic regulators. It is believed that the anti-inflammatory actions of glucocorticoids are predominantly based on gene repression whereas many unwanted side-effects of steroid treatment (such as hyperglycemia and obesity) are due to transcriptional activation. Yet how the GR activates some genes while potently repressing others, remains an unresolved molecular paradox. Current models for suppression favor either trans-repression, with GR 'tethering' to AP-1/NF-κB, association with inhibitory nGREs, or recruitment of the corepressor GRIP1. Using genomic analyses in LPS-stimulated macrophages, we show that upon TLR4 activation, the GR cistrome features classical GREs together with NF-κB and AP-1 motifs at both up- and down-regulated genes, excluding the concept that these factors oppose each other. Surprisingly, tethered sites, GREs and GRIP1 support positive as well as negative regulation. Classical models hence fail to predict the polarity of GR regulation. Interestingly, negative enhancers appear to be correlated with IRF3 occupancy. These sites utilize GRIP1's corepressor function and are characterized by reduced histone acetylation patterns. This implies that transcriptional outcome is established by epigenetic regulators and context rather than sequence and suggests the existence of unrecognized regulatory determinants.
Molecular Characterization of a Saline‐Soluble Lectin from a Parasitic Fungus (1996)

It has been proposed that the interactions between several parasitic and pathogenic fungi and their hosts are mediated by soluble lectins present in the fungus. We have cloned and analyzed a gene encoding such a lectin (AOL) from the nematophagous fungus Arthrobotrys oligospora (deuteromycete). The deduced primary structure of the AOL gene displayed an extensive similarity (identity 46.3%) to that of a gene encoding a lectin (ABL) recently isolated from the mushroom Agaricus bisporus (basidiomycete), but not to any other fungal, microbial, plant or animal lectins. The similarities between AOL and ABL were further demonstrated by the observation that an antibody specific for AOL cross-reacted with ABL. Together with data showing that AOL has a binding specificity that is similar to that of ABL [Rosen, S., Bergström, J., Karlsson, K.-A. & Tunlid, A. (1996) Eur. J. Biochem. 238, 830-837], these results indicate that AOL and ABL are members of a novel family of saline soluble lectins present in fungi. Southern blots indicated that there is only one AOL gene in the genome encoding a subunit (monomer) of the lectin. The primary structure of AOL did not show the presence of a typical N-terminal signal sequence. Comparison of the deduced primary structure with the molecular mass of AOL as determined by electrospray mass spectrometry (16153 Da), indicated that AOL has an acetylated N-terminal but no other post-translational modifications, and that a minor isoform is formed by deamidation. Circular dichroism (CD) spectroscopy suggested that the secondary structure of AOL contains 34% beta-sheets, 21% alpha-helix, and 45% turns and coils.