gebhart/patrepeval huggingface dataset:
The association between deficient manganese levels and breast cancer: a meta-analysis. (2015)

There are conflicting reports on the correlation between manganese (Mn) levels and breast cancer. The purpose of the present study is to clarify the association between Mn levels and breast cancer using a meta-analysis approach. We searched articles indexed in Pubmed and the Chinese Journal Full-text Database (CJFD) published as of August 2014 that met our predefined criteria. Eleven eligible studies involving 1302 subjects were identified. Overall, pooled analysis indicated that subjects with breast cancer had lower Mn levels than the healthy controls (SMD = -1.51, 95% CI = [-2.47, -0.56]). Further subgroup analysis found a similar pattern in China (SMD = -1.32, 95% CI = [-2.33, -0.32]) and Korea (SMD = -4.08, 95% CI = [-4.63, -3.54]), but not in Turkey (SMD = -0.96, 95% CI = [-3.19, 1.27]). Further subgroup analysis also found a similar pattern in different sample specimens (serum: SMD = -1.24, 95% CI = [-2.31, -0.16]; hair: SMD = -1.99, 95% CI = [-3.91, -0.06]) and different types of Mn measurement (inductively coupled plasma-atomic absorption spectrometry (ICP-AAS): SMD = -1.14, 95% CI = [-2.24, -0.04]; graphite furnace atomic absorption spectroscopy (GFAAS): SMD = -1.94, 95% CI = [-2.38, -1.49]; inductively coupled plasma-atomic emission spectrometry (ICP-AES): SMD = -3.77, 95% CI = [-4.70, -2.85]). No evidence of publication bias was observed. In conclusion, this meta-analysis supports a significant association between deficient Mn levels and breast cancer. However, the subgroup analysis found that there was contradiction regarding races and geography, like China and Turkey. Thus this finding needs further confirmation by trans-regional multicenter, long-term observation in a cohort design to obtain better understanding of causal relationships between Mn levels and breast cancer, through measuring Mn at baseline to investigate whether the highest Mn category versus lowest was associated with breast cancer risk.
Historical Study on Factors Inducing Soil-Transmitted Helminth Infection among People of Old Seoul City during Joseon Dynasty (2013)

In a series of paleo-parasitological investigations, we have been able to obtain invaluable data on parasite infection patterns prevalent among the Joseon (1392-1910) people in Korea. Thus far we have established that the Joseon people were in fact heavily infected by various species of parasites, though precise patterns and exact statuses of infection in specific town and cities have proved elusive. In the present study, relevant historical documentation was obtained and examined, shedding light on some of the operative socio-cultural factors that might have played a role in inducing a high infection prevalence of Ascaris, a soil-transmitted roundworm, in Joseon society. On this evidentiary basis, we could confirm that the recycling of human feces as fertilizer and the habit of eating raw vegetables were both closely related to infection. These factors were sufficient to maintain the life cycle of Ascaris, there by perpetuating a cycle of infection and reinfection among the Joseon inhabitants. Overall, this study demonstrated the value of close medical-scientist / historian interdisciplinary collaboration infacilitating comprehensive and meaningful paleo-parasitological findings and interpretations.
A novel application of time-reversed acoustics: Salt-dome flank imaging using walkaway VSP surveys (2006)

Abstract In this paper we present initial results of applying Time-Reversed Acoustics (TRA) technology to salt-dome flank, seismic imaging. We created a set of synthetic traces representing a multilevel, walkaway VSP for a model composed of a simplified Gulf of Mexico vertical-velocity gradient and an embedded salt dome. We first applied the concepts of TRA to the synthetic traces to create a set of redatummed traces without having to perform velocity analysis, moveout corrections, or complicated processing. Each redatummed trace approximates the output of a zero-offset, downhole source and receiver pair. To produce the final salt-dome flank image, we then applied conventional, poststack, depth migration to the zero-offset section. Our results show a very good image of the salt when compared to an image derived using data from a downhole, zero-offset source and receiver pairs. The simplicity of our TRA implementation provides a virtually automated method to estimate a zero-offset, seismic section as if it had been collected from the reference frame of the borehole containing the VSP survey.
Thermo-optical bistability with Si nanocrystals in a whispering gallery mode resonator (2013)

We report on the observation of optical bistability in an integrated planar microresonator with embedded silicon nanocrystals (Si-ncs). The phenomenon originates from the thermo-optical modulation of the silica-embedded Si-ncs refractive index, which in turn alters the spectral position of the resonator mode. The estimated thermo-optical coefficient of the Si nanocrystalline material, dn/dT≈2.92×10(-5)> K(-1), is an order of magnitude lower than that of bulk silicon. Both time-resolved pump-and-probe experiments and numerical simulations confirm that the silica host is responsible for the heat dissipation from the resonator. Moreover, a negligible Q-factor degradation at pump powers as high as 100 mW, along with the absence of a fast component in time-resolved measurements, confirm the minute contribution from excited carriers effects. These observations, combined with the already published large third-order nonlinearities of Si-ncs (an order of magnitude larger than in bulk Si), make this system an outstanding candidate for low-power on-chip nonlinear comb generation.
Ultraselective fluorescent sensing of Hg2+ through metal coordination-induced molecular aggregation (2008)

A new type of fluorescent sensor has been developed from a perylene based molecule, N,N'-dideoxythymidine-3,4,9,10-perylene-tetracarboxylic diimide (TT-PTCDI); the strong, highly selective binding between the thymine ligand (T) and Hg2+ ion enables efficient sensing of mercury ions based on a fluorescence quenching mechanism, which is primarily caused by metal-coordination induced molecular aggregation.
Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi (2010)

Borrelia burgdorferi is a causative agent of Lyme disease in North America and Eurasia. The first complete genome sequence of B. burgdorferi strain 31, available for more than a decade, has assisted research on the pathogenesis of Lyme disease. Because a single genome sequence is not sufficient to understand the relationship between genotypic and geographic variation and disease phenotype, we determined the whole-genome sequences of 13 additional B. burgdorferi isolates that span the range of natural variation. These sequences should allow improved understanding of pathogenesis and provide a foundation for novel detection, diagnosis, and prevention strategies.
Application of the New Generation of Sequencing Technologies for Evaluation of Genetic Consistency of Influenza A Vaccine Viruses (2016)

For almost half a century, Sanger sequencing has been the conventional method for sequencing DNA. However, its utility for sequencing heterogeneous viral populations is limited because it can only detect mutations that are present in a significant portion of the DNA molecules. Several molecular methods that quantify mutations present at low levels in viral populations were proposed for evaluation of genetic consistency of viral vaccines; however, these methods are only suitable for single site polymorphisms, and cannot be used to screen for unknown mutations.
Oxymorphone Extended-Release Tablets Relieve Moderate to Severe Pain and Improve Physical Function in Osteoarthritis: Results of a Randomized, Double-Blind, Placebo- and Active-Controlled Phase III Trial (2005)

In this short-term study, oxymorphone ER was superior to placebo for relieving pain and improving function in patients with moderate to severe chronic OA pain, and is an alternative to other sustained-release opioids.
Unique Epitopes on CεmX in IgE–B Cell Receptors Are Potentially Applicable for Targeting IgE-Committed B Cells (2010)

Abstract Membrane-bound IgE (mIgE) is part of the IgE–BCR and is essential for generating isotype-specific IgE responses. On mIgE+ B cells, the membrane-bound ε-chain (mε) exists predominantly in the long isoform, mεL, containing an extra 52 aa CεmX domain between CH4 and the C-terminal membrane-anchoring segment; the short isoform of mε, mεS, exists in minor proportions. CεmX thus provides an attractive site for immunologic targeting of mIgE+ B cells. In this study, we show that nine newly prepared CεmX-specific mAbs, as well as the previously reported a20, bound to mIgE.FcL-expressing CHO cells, while only 4B12 and 26H2 bound to mIgE.FcL-expressing B cell line Ramos cells. The mAb 4B12 bound to the N-terminal part, 26H2 the middle part, and all others the C-terminal part of CεmX. Expression of Igα and Igβ on the mIgE.FcL-CHO cells reduces the binding of a20 to CεmX as compared with that of 4B12 and 26H2. The chimeric mAbs c4B12 and c26H2, when cross-linked by secondary antibodies, lysed mIgE.FcL-Ramos cells by apoptosis through a BCR-dependent caspase pathway. Using PBMCs as the source of effector cells, c4B12 and c26H2 demonstrated Ab-dependent cellular cytotoxicity toward mIgE.FcL-Ramos cells in a dose-dependent fashion. In cultures of PBMCs from atopic dermatitis patients, c4B12 and c26H2 inhibited the synthesis of IgE driven by anti-CD40 and IL-4. These results suggest that 4B12 and 26H2 and an immunogen using the peptide segments recognized by these mAbs are potentially useful for targeting mIgE+ B cells to control IgE production.
<title>Phase difference method for target motion compensation of stepped-frequency ISAR signatures</title> (1996)

In this article, we present a method for estimating the translational motion parameters of a target from its ISAR signature. The method exploits the phase of the target's frequency response and does not require 2D Fourier processing. The basis for this method is a phase difference indicator which converges to an absolute minimum when the phase is compensated with the true values of the motion parameters. The analysis of the phase difference indicator leads to an algorithm for motion parameter optimization. Processing of simulated and experimental ISAR signatures demonstrates that the phase difference method is extremely computationally efficient and equally accurate when compared to robust techniques based on entropy or Fisher information indicators.
In Vivo Microvascular Pattern of Solitary Juxtapapillary Capillary Hemangioma on OCT Angiography (2017)

Juxtapapillary capillary hemangioma (JCH) is a vascular hamartoma. Fluorescein fundus angiography aids in diagnosis. The vascular morphology of this tumor has not been documented with optical coherence tomography angiography (OCTA), a new, noninvasive diagnostic modality that provides high-resolution images of vascular pattern based on blood flow in the retina and choroid. Although mainly a clinical diagnosis, OCTA helps in studying the intrinsic vascularity of the tumor and helps in differentiating it from other vascular tumors. The authors report the case of a young male with unilateral solitary JCH and its microvascular pattern, as seen on OCTA. [ Ophthalmic Surg Lasers Imaging Retina. 2017;48:592–595. ]
The Rho-associated protein kinase p160ROCK is required for centrosome positioning (2002)

The p160-Rho-associated coiled-coil-containing protein kinase (ROCK) is identified as a new centrosomal component. Using immunofluorescence with a variety of p160ROCK antibodies, immuno EM, and depletion with RNA interference, p160ROCK is principally bound to the mother centriole (MC) and an intercentriolar linker. Inhibition of p160ROCK provoked centrosome splitting in G1 with the MC, which is normally positioned at the cell center and shows little motion during G1, displaying wide excursions around the cell periphery, similar to its migration toward the midbody during cytokinesis. p160ROCK inhibition late after anaphase in mitosis triggered MC migration to the midbody followed by completion of cell division. Thus, p160ROCK is required for centrosome positioning and centrosome-dependent exit from mitosis.
Data from iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type–Specific Markers of Immune-Cell Infiltration (2023)

&lt;div&gt;Abstract&lt;p&gt;The development of immune checkpoint–based immunotherapies has been a major advancement in the treatment of cancer, with a subset of patients exhibiting durable clinical responses. A predictive biomarker for immunotherapy response is the preexisting T-cell infiltration in the tumor immune microenvironment (TIME). Bulk transcriptomics–based approaches can quantify the degree of T-cell infiltration using deconvolution methods and identify additional markers of inflamed/cold cancers at the bulk level. However, bulk techniques are unable to identify biomarkers of individual cell types. Although single-cell RNA sequencing (scRNA-seq) assays are now being used to profile the TIME, to our knowledge there is no method of identifying patients with a T-cell inflamed TIME from scRNA-seq data. Here, we describe a method, iBRIDGE, which integrates reference bulk RNA-seq data with the malignant subset of scRNA-seq datasets to identify patients with a T-cell inflamed TIME. Using two datasets with matched bulk data, we show iBRIDGE results correlated highly with bulk assessments (0.85 and 0.9 correlation coefficients). Using iBRIDGE, we identified markers of inflamed phenotypes in malignant cells, myeloid cells, and fibroblasts, establishing type I and type II interferon pathways as dominant signals, especially in malignant and myeloid cells, and finding the TGFβ-driven mesenchymal phenotype not only in fibroblasts but also in malignant cells. Besides relative classification, per-patient average iBRIDGE scores and independent RNAScope quantifications were used for threshold-based absolute classification. Moreover, iBRIDGE can be applied to &lt;i&gt;in vitro&lt;/i&gt; grown cancer cell lines and can identify the cell lines that are adapted from inflamed/cold patient tumors.&lt;/p&gt;&lt;/div&gt;
#VisualHashtags (2017)

The data generated on social media sites continues to grow at an increasing rate with more than 36% of tweets containing images making the dominance of multimedia content evidently visible. This massive user generated content has become a reflection of world events. In order to enhance the ability and effectiveness to consume this plethora of data, summarization of these events is needed. However, very few studies have exploited the images attached with social media events to summarize them using "mid-level visual elements". These are the entities which are both representative and discriminative to the target dataset besides being human-readable and hence more informative.
4.3: SWNT fiber field emission cathodes (2010)

Small diameter, high current density electron beams are needed for the small beam tunnels required for high frequency traveling wave tube (TWT) amplifiers. The Air Force Research Laboratory (AFRL) began research on small diameter (<;100μm) single fiber DC cathodes for this application. Two types of fibers were tested. Fibers made from graphite were compared to fibers made solely from single walled carbon nanotubes (SWNTs) that are densely packed and highly aligned along the axial direction. Graphite fiber cathodes suffered serious degradation due to joule heating after only 25 hours of operation while only producing up to 200μA of current. SWNT fiber cathodes produced approximately 3mA of current for hundreds of hours while showing minimal physical damage.
Observation of B[superscript +][subscript c] → D[superscript 0]K[superscript +] Decays (2017)

Using proton-proton collision data corresponding to an integrated luminosity of 3.0 fb[superscript -1], recorded by the LHCb detector at center-of-mass energies of 7 and 8 TeV, the B[superscript +][subscript c] → D[superscript 0]K[superscript +] decay is observed with a statistical significance of 5.1 standard deviations. By normalizing to B[superscript +] →[bar over D][superscript 0]π[superscript +] decays, a measurement of the branching fraction multiplied by the production rates for B[superscript +][subscript c] relative to B[superscript +] mesons in the LHCb acceptance is obtained, R[subscript D[superscript 0]K] =(f[subscript c]/f[subscript u])×B(B[superscript +][subscript c] →D[superscript 0]K[superscript +]) =(9.3[superscript +2.8][subscript -2.5] ± 0.6) × 10[superscript -7], where the first uncertainty is statistical and the second is systematic. This decay is expected to proceed predominantly through weak annihilation and penguin amplitudes, and is the first B[superscript +][subscript c] decay of this nature to be observed.
Event-Driven Approach for Flow-to-Core Mapping by NICs in Multicore Systems (2016)

In exploiting multiple cores for packet processing, steering incoming packets to the same core on which its application resides is important for the performance issue. One of the key components for this is flow-to-core mapping table, which is used by NIC to steer incoming packets to right cores. To acquire the information required for flow-to-core table, we propose an event-driven approach unlike existing technologies, which take per-packet-based approach and thus cause non-negligible overhead. In addition, exploiting standard Linux utility to manipulate flow-to-core table of NIC, we realize NIC-independent approach unlike existing technologies, which require specific NICs.
Evaluation of dermal segment on viscoelasticity measurement of skin by rheometer (2007)

The engineering of human tissue represents a major technique in clinical medicine. Material evaluation of skin is important as preventive medicine. Decubitus originates in pressure and the rub. However, shearing in the skin has exerted the influences on the sore pressures most. This paper examines one demand of crucial importance, namely the real time in vivo monitoring of the shearing characteristics skin tissue. Rheometer is a technology developed to measure viscoelasticity of solid and liquid. To measure viscoelasticity of the skin in the noninvasive with this device, we remodeled it. It is ideal for the continuous monitoring of tissues in vivo.
Synthesis and properties of highly refractive polyimides derived from fluorene‐bridged sulfur‐containing dianhydrides and diamines (2007)

Abstract Highly refractive and transparent polyimides (PIs) based on fluorene‐bridged and sulfur‐containing monomers have been developed. An aromatic dianhydride, 4,4′‐[ p ‐thiobis(phenylenesulfanyl)]diphthalic anhydride (3SDEA), was polymerized with several fluorene‐containing diamines, including commercially available 9,9′‐bis( p ‐aminophenyl)fluorene (APF), 9,9′‐bis[4‐( p ‐aminophenoxy)phenyl]fluorene (OAPF), and newly synthesized 9,9′‐bis[4‐( p ‐aminophenyl)sulfanylphenyl]fluorene (ASPF) to afford series A PIs. Meanwhile, series B PIs were obtained from a new dianhydride, 4,4′‐[(9H‐fluorene‐9‐ylidene)bis( p ‐phenylsulfanyl)]diphthalic anhydride (FPSP) and two aromatic diamines, ASPF and 4,4′‐thiobis[( p ‐phenylenesulfanyl)aniline] (3SDA) via a two‐step polycondensation procedure. The PIs exhibit good thermal stabilities, such as relatively high glass transition temperatures in the range of 220–270 °C and high initial thermal decomposition temperatures ( T 10% ) exceeding 490 °C. The 9,9′‐disubstituted fluorene moieties endow the PI films with good optical transparency. The optical transmittances of the PI films at 450 nm are all higher than 80% for the thickness of about 10 μm. Furthermore, the highly aromatic fluorene moiety and flexible thioether linkages in the molecular chains of the PIs provide them with high refractive indices of 1.6951–1.7258 and small birefringence of 0.0056–0.0070. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1510–1520, 2008
Expressive languages for path queries over graph-structured data (2010)

For many problems arising in the setting of graph querying (such as finding semantic associations in RDF graphs, exact and approximate pattern matching, sequence alignment, etc.), the power of standard languages such as the widely studied conjunctive regular path queries (CRPQs) is insufficient in at least two ways. First, they cannot output paths and second, more crucially, they cannot express relations among paths.
EXPERIMENTAL AND NUMERICAL INVESTIGATION OF ACTIVE FLOW CONTROL ON A GENERIC TRUCK CABIN (2016)

This work presents the achievement in drag reduction by use of Active Flow Control (AFC) on a generic bluff body. The model consists of a simplified truck cabin, characterized by sharp edge separation on top and bottom edges and pressure induced separation on the rounded vertical front corner. The pressure induced separation reproduces the flow separation occurring at the front A-pillar of a real truck.Hybrid Partially Averaged Navier-Stokes (PANS) simulations are compared with wind tunnel experiments.The Reynolds number for both simulations and experiments is Re = 5×10^5 based on the inlet velocity Uinf and the width of the model W = 0.4 m. A validation of the hybrid CFD model on two flow configurations is followed by a CFD study on the optimal actuation frequency able to minimize the aerodynamic drag. PANS accurately predicts the flow field measured in experiments and a notable drag reduction by means of AFC is observed in a numerical study.
Intermolecular Interaction in Multicomponent Supramolecular Complexes through Hydrogen-Bonding Association (2002)

A series of main-chain hydrogen-bonded supramolecular complexes have been prepared by self-assembly of proton donor (diacid) and acceptor (bipyridyl ethylene) through the formation of intermolecular hydrogen bonds. The phase transition behaviors were studied using differential scanning calorimetry and polarized optical microscopy. X-ray photoelectron spectroscopy study indicated that the binding energy of N 1s upshifted ca. 0.8 eV, which was within the limit of the hydrogen-bonding interaction. Solid-state CP/MAS 13C NMR spectroscopy experiments revealed that an induced upfield shift (Δδ ≥ 4 ppm) of carbonyl carbon in solid state was observed as a result of the formation of intermolecular hydrogen bond. The natural abundance CP/MAS 15N NMR spectroscopy also supported that the molecular complexes with hydrogen bond characteristics rather than zwitterionic complexes were formed on the basis of the change in 15N chemical shift.
Molecular Properties, Functional Mechanisms, and Applications of Sliced siRNA (2015)

Using pre-miR-451 as a model molecule, we have characterized the general molecular properties of small hairpin RNAs that are processed into potent small interfering RNAs (siRNA) by Argonaute2 (Ago2). The Ago2-sliced siRNAs (sli-siRNAs) have the same silencing potency as the classical Dicer diced siRNAs (di-siRNAs) but have dramatically reduced unwanted sense strand activities. We have built vectors with the constitutive or inducible U6 promoter that can express sli-siRNAs in mammalian cells, in which the sli-siRNAs can be correctly processed to repress target genes. As a proof of principle for potential applications of sli-siRNAs in vivo, we show that the expression of one Ago2 shRNA-1148 in HCT-116 colon cancer cells knocked down RRM2 expression and reduced the proliferation and invasiveness of the cells. The defined sli-siRNA model molecules and the expression systems established in this study will facilitate the design and application of sli-siRNAs as novel potent RNAi triggers with reduced off-target effects.