gebhart/patrepeval huggingface dataset:
Persistent Infection of Thymic Epithelial Cells with Coxsackievirus B4 Results in Decreased Expression of Type 2 Insulin-Like Growth Factor (2012)

It has been hypothesized that a disturbance of central self-tolerance to islet β cells may play a role in the enteroviral pathogenesis of type 1 diabetes. Whether enteroviruses can induce an impaired expression of β-cell self-antigens in thymic epithelial cells has been investigated in a murine thymic epithelial (MTE) cell line. This cell line was permissive to the diabetogenic group B4 coxsackievirus (CV-B4) strain CV-B4 E2 and spontaneously expressed type 2 insulin-like growth factor (Igf2), the dominant self-antigen of the insulin family. In this model, a persistent replication of CV-B4 E2 was obtained, as attested to by the prolonged detection of intracellular positive- and negative-strand viral RNA by reverse transcription-PCR (RT-PCR) and capsid protein VP1 by immunofluorescent staining and by the release of infectious particles in culture supernatants. The chronic stage of the infection was characterized by a low proportion of VP1-positive cells (1 to 2%), whereas many cells harbored enteroviral RNA, as displayed by RT-PCR without extraction applied directly to a few cells. Igf2 mRNA and IGF-2 protein were dramatically decreased in CV-B4 E2-infected MTE cell cultures compared with mock-infected cultures, whereas housekeeping and interleukin-6 (Il6) gene expression was maintained and Igf1 mRNA was decreased, but to a lower extent. Inoculation of CV-B3, CV-B4 JVB, or echovirus 1 resulted in a low level of IGF-2 in culture supernatants as well, whereas herpes simplex virus 1 stimulated the production of the protein. Thus, a persistent infection of a thymic epithelial cell line with enteroviruses like CV-B4 E2 can result in a disturbed production of IGF-2, a protein involved in central self-tolerance toward islet β cells.
Repifermin (keratinocyte growth factor‐2) for the treatment of active ulcerative colitis: a randomized, double‐blind, placebo‐controlled, dose‐escalation trial (2003)

Intravenous repifermin at a dose of 1-50 microg/kg was very well tolerated, but there was no evidence that repifermin was effective for the treatment of active ulcerative colitis at these doses. An additional study to determine the efficacy of repifermin at doses of > 50 microg/kg or for a longer treatment duration may be warranted, as the maximally tolerated dose was not reached in the present study.
SHOULDER ARTHROPLASTY FOR OSTEOARTHRITIS SECONDARY TO GLENOID DYSPLASIA (2002)

The data from this study suggest that glenoid deficiency and cartilage wear should be addressed in some way at the time of shoulder arthroplasty in patients with glenoid dysplasia.
Performance-Based Path Selection for Explicitly Routed Label Switched Paths (LSPs) Using TE Metric Extensions (2016)

In certain networks, it is critical to consider network performance criteria when selecting the path for an explicitly routed RSVP-TE Label Switched Path (LSP). Such performance criteria can include latency, jitter, and loss or other indications such as the conformance to link performance objectives and non-RSVP TE traffic load. This specification describes how a path computation function may use network performance data, such as is advertised via the OSPF and IS-IS TE metric extensions (defined outside the scope of this document) to perform such path selections.
Cloning and expression in streptomyces lividans of antibiotic resistance genes derived from Escherichia coli (1981)

Hybrid plasmids that replicate in both Escherichia coli and Streptomyces lividans were constructed in vitro by joining the E. coli-derived plasmid pACYC184 or pACYC177, at their BamHI or PstI restriction site, respectively, to S. lividans plasmid pSLP111. After introduction of the composite replicons into S. lividans by transformation, chloramphenicol (Cm) resistance encoded by pACYC184 and kanamycin resistance encoded by pACYC177 were phenotypically expressed in the S. lividans host. A Sau3A restriction endonuclease-generated deoxyribonucleic acid fragment from pACYC184 containing the entire structural gene for the Cm acetyltransferase enzyme, but lacking the nucleotide sequence ordinarily serving as the Cm resistance gene promoter, also specified resistance to Cm when introduced in either orientation into the BamHI or BclI endonuclease cleavage site of pSLP111 or into corresponding sites of the analogous plasmid pSLP101. These findings make it unlikely that the biologically active CM acetyltransferase was being made in S. lividans as part of a fused protein, but instead indicate that the ATG start codon used for initiation of translation of the Cm resistance gene in E. coli was also utilized in S. lividans. In contrast, the synthesis of messenger ribonucleic acid that encodes the Cm acetyltransferase in S. lividans was, in at least one instance, apparently initiated at nucleotide sequences within the S. lividans plasmid vector, with resulting transcriptional read-through into the E. coli-derived deoxyribonucleic acid segment.
Chopping Frequency Variation of Photoacoustic Amplitude from Porous Silicon (2000)

We investigated the possibility of applying photoacoustic (PA) spectroscopy to the study of luminescent porous silicon. Since porous silicon is usually formed on a silicon substrate, PA spectroscopy is useful for obtaining the absorption coefficient of porous silicon without removing the substrate. In this article, we investigated the chopping frequency dependence of the PA signal from porous silicon and showed that the chopping frequency is critical for the exclusion of the PA signal from silicon substrate.
Dynamics of the Human Antibody Repertoire following B-cell Depletion in Systemic Sclerosis (2017)

Abstract Systemic sclerosis with pulmonary arterial hypertension (SSc-PAH) is a debilitating and frequently lethal disease of unknown cause lacking effective treatment options. Lymphocyte anomalies and autoantibodies observed in systemic sclerosis have suggested an autoimmune character. Here we study the clonal structure of the B-cell repertoire in SSc-PAH using immunoglobulin heavy-chain sequencing before and after B-cell depletion. We found SSc-PAH to be associated with anomalies in B-cell development, namely altered VDJ rearrangement frequencies (reduced IGHV2-5 segment usage) and an increased somatic mutation-fixation probability in expanded B-cell lineages. SSc-PAH was also characterized by anomalies in B-cell homeostasis, namely an expanded IgD + proportion with reduced mutation loads and an expanded proportion of highly antibody-secreting cells. Disease signatures pertaining to IGHV2-5 segment usage, IgD proportions and mutation loads were temporarily reversed after B-cell depletion. Analyzing the time course of B-cell depletion, we find that the kinetics of naïve replenishment are predictable from baseline measurements alone, that release of plasma cells into the periphery can precede naïve replenishment and that modes of B-cell receptor diversity are highly elastic. Our findings shed light on the humoral immune basis of SSc-PAH and provide insights into the effect of B-cell depletion on the antibody repertoire. Abbreviations SSc-PAH Systemic sclerosis with pulmonary arterial hypertension IGH immunoglobulin heavy-chain BCR B-cell receptor CDR3 complementarity-determining region 3 Ig immunoglobulin AA amino acid
On the impact of small cell discovery mechanisms on device power consumption over LTE networks (2013)

Small Cells are under extensive investigation as a potential solution to meet the increasing capacity demand due to ever growing data traffic over cellular networks. The architecture of small cells is still under discussion, various architectures have been proposed based on potential use cases. One of the most important use cases is to deploy small cells on a different frequency than that of the macro cell to offload traffic. Small cell discovery in this type of inter-frequency scenario is an open research problem. Aggressive scanning mechanisms may result in faster discovery of small cells and higher user throughput as well as higher macro cell capacity due to potentially increased offloading opportunity. However, frequent scanning may also result in higher power consumption for the device. Therefore, a tradeoff between offloading opportunity and device power consumption seems inevitable in practice. In this paper, we analyze the trade-off between the offloading capacity and device power consumption due to inter-frequency scanning mechanism for small cell discovery. Our findings show that although increasing the frequency of inter-frequency scanning does result in increased power consumption due to scanning, it actually lowers the total power consumed by the device since it leads to offloading to small cells, where the device consumes less overall power due to better coverage.
Engineered Culture Models for Studies of Tumor-Microenvironment Interactions (2013)

Heterogeneous microenvironmental conditions play critical roles in cancer pathogenesis and therapy resistance and arise from changes in tissue dimensionality, cell-extracellular matrix (ECM) interactions, soluble factor signaling, oxygen as well as metabolic gradients, and exogeneous biomechanical cues. Traditional cell culture approaches are restricted in their ability to mimic this complexity with physiological relevance, offering only partial explanation as to why novel therapeutic compounds are frequently efficacious in vitro but disappoint in preclinical and clinical studies. In an effort to overcome these limitations, physical sciences-based strategies have been employed to model specific aspects of the cancer microenvironment. Although these strategies offer promise to reveal the contributions of microenvironmental parameters on tumor initiation, progression, and therapy resistance, they, too, frequently suffer from limitations. This review highlights physicochemical and biological key features of the tumor microenvironment, critically discusses advantages and limitations of current engineering strategies, and provides a perspective on future opportunities for engineered tumor models.
Sensitivity and Detection Problems (2016)

In this chapter, receiver sensitivity is discussed. The sensitivity of a receiver is defined as its ability to measure the weakest signal. The output of an analog-to-digital converter (ADC) is digital. This output impacts the measurement approach of input signals and thus receiver sensitivity. The conventional way to calculate sensitivity is through mathematical modeling. However, due to the nonlinear property ADCs, it is difficult to manipulate the calculations mathematically. As a result, the basic analysis is still based on an analog approach. If the ADC has a large number of bits, the result will be close to the analog approach. The threshold for detecting false alarms and signals in a digital receiver cannot be set arbitrarily in a continuous sense. The threshold can only be chosen from a finite number of levels. This chapter discusses different types of detection schemes. The difference between the detection schemes of analog and digital receivers is emphasized. The possible advantages of a digital receiver from a detection point of view are discussed. The detection based on one data sample is discussed first. The one-sample case is then extended to multiple samples. Finally, frequency domain detection, which can be applied to digital receivers, is examined. Examples with computer programs are used to illustrate some of the detection schemes. Before the general discussion, let us clarify the meaning of the word detection. This word has two distinct applications in a discussion of receivers. In the first sense, it refers to the process of converting a radio frequency (RF) signal or noise into a video signal. In the second sense, it refers to the process that determines whether a signal is present. In spite of this ambiguity, the meaning should be clear from the context.
Tailor-made 3D dosimeter using 3D printing technology (2020)

This article reports initial results of fabricating a tailor-made 3D dosimeter using radiochromic material and a 3D printer. The 3D dose distribution is easily visualized and quantitated as the transparent polymers become colored after irradiation. With this technology, we propose a novel method that uses 3D dosimetry to precisely copy the shape of human organs with our 3D printed dosimeter and help provide more accurate and safe radiotherapy.
Enhanced Electrochemical Catalytic Efficiencies of Electrochemically Deposited Platinum Nanocubes as a Counter Electrode for Dye-Sensitized Solar Cells (2015)

Platinum nanocubes (PtNCs) were deposited onto a fluorine-doped tin oxide glass by electrochemical deposition (ECD) method and utilized as a counter electrode (CE) for dye-sensitized solar cells (DSSCs). In this study, we controlled the growth of the crystalline plane to synthesize the single-crystal PtNCs at room temperature. The morphologies and crystalline nanostructure of the ECD PtNCs were examined by field emission scanning electron microscopy and high-resolution transmission electron microscopy. The surface roughness of the ECD PtNCs was examined by atomic force microscopy. The electrochemical properties of the ECD PtNCs were analyzed by cyclic voltammetry, Tafel polarization, and electrochemical impedance spectra. The Pt loading was examined by inductively coupled plasma mass spectrometry. The DSSCs were assembled via an N719 dye-sensitized titanium dioxide working electrode, an iodine-based electrolyte, and a CE. The photoelectric conversion efficiency (PCE) of the DSSCs with the ECD PtNC CE was examined under the illumination of AM 1.5 (100 mWcm(-2)). The PtNCs in this study presented a single-crystal nanostructure that can raise the electron mobility to let up the charge-transfer impedance and promote the charge-transfer rate. In this work, the electrocatalytic mass activity (MA) of the Pt film and PtNCs was 1.508 and 4.088 mAmg(-1), respectively, and the MA of PtNCs was 2.71 times than that of the Pt film. The DSSCs with the pulse-ECD PtNC CE showed a PCE of 6.48 %, which is higher than the cell using the conventional Pt film CE (a PCE of 6.18 %). In contrast to the conventional Pt film CE which is fabricated by electron beam evaporation method, our pulse-ECD PtNCs maximized the Pt catalytic properties as a CE in DSSCs. The results demonstrated that the PtNCs played a good catalyst for iodide/triiodide redox couple reactions in the DSSCs and provided a potential strategy for electrochemical catalytic applications.
A Portable High-Resolution Surface Measurement Device (2012)

A high-resolution portable surface measurement device has been demonstrated to provide micrometer-resolution topographical plots. This device was specifically developed to allow in situ measurements of defects on the Space Shuttle orbiter windows but is versatile enough to be used on a wide variety of surfaces. This paper discusses the choice of an optical sensor and then the decisions required to convert a laboratory bench optical measurement device into an ergonomic portable system. The necessary tradeoffs between performance and portability are presented along with a description of the device developed to measure orbiter window defects.
Preferential metabolism of N-nitrosodiethylamine by two cell lines derived from human pulmonary adenocarcinomas (1986)

Diethylnitrosamine (DEN), in common with other nitrosamines, is a carcinogenic agent which produces tumors in a wide variety of tissues in experimental animals. The pulmonary Clara cell is a major target of N-nitrosamine-induced carcinogenesis in hamsters and rats. DEN is believed to require metabolic activation to elicit its carcinogenic effects. The metabolism of [14C]DEN was studied in two cell lines derived from human lung adenocarcinomas and two cell lines derived from human small cell lung cancers by monitoring 14CO2 production and covalent binding of radiolabel from [14C]DEN to the cell protein and DNA fractions. [14C]DEN was metabolized by adenocarcinoma-derived NCI-H322 (with Clara cell features) and NCI-H358 (with features of alveolar type II cells) but not by NCI-H69 and NCI-H128 (derived from small cell carcinoma). Metabolism was markedly inhibited by heat denaturation of the cell protein. [14C]DEN metabolism by NCI-H322 was greatly decreased when the incubation was carried out under anaerobic conditions and in the presence of a carbon monoxide enriched atmosphere. These results suggested the involvement of the cytochrome P-450-dependent monooxygenase enzyme system. Metabolism by NCI-H358 was also decreased in the absence of oxygen or presence of carbon monoxide although the effects were relatively small compared with the results with NCI-H322. On the other hand, aspirin or indomethacin, which are inhibitors of the fatty acid cyclooxygenase component of prostaglandin endoperoxide synthetase, preferentially inhibited [14C]DEN metabolism by NIC-H358. There were little or no effects of these inhibitors on the metabolism of DEN in NCI-H322. The data suggest that DEN metabolism in different lung cell types may be carried out by different enzyme systems which in turn may contribute to the selective effect of DEN in the lung.
Key Molecular Factors in Hemagglutinin and PB2 Contribute to Efficient Transmission of the 2009 H1N1 Pandemic Influenza Virus (2012)

Animal influenza viruses pose a clear threat to public health. Transmissibility among humans is a prerequisite for a novel influenza virus to cause a human pandemic. A novel reassortant swine influenza virus acquired sustained human-to-human transmissibility and caused the 2009 influenza pandemic. However, the molecular aspects of influenza virus transmission remain poorly understood. Here, we show that an amino acid in hemagglutinin (HA) is important for the 2009 H1N1 influenza pandemic virus (2009/H1N1) to bind to human virus receptors and confer respiratory droplet transmissibility in mammals. We found that the change from glutamine (Q) to arginine (R) at position 226 of HA, which causes a switch in receptor-binding preference from human α-2,6 to avian α-2,3 sialic acid, resulted in a virus incapable of respiratory droplet transmission in guinea pigs and reduced the virus's ability to replicate in the lungs of ferrets. The change from alanine (A) to threonine (T) at position 271 of PB2 also abolished the virus's respiratory droplet transmission in guinea pigs, and this mutation, together with the HA Q226R mutation, abolished the virus's respiratory droplet transmission in ferrets. Furthermore, we found that amino acid 271A of PB2 plays a key role in virus acquisition of the mutation at position 226 of HA that confers human receptor recognition. Our results highlight the importance of both the PB2 and HA genes on the adaptation and transmission of influenza viruses in humans and provide important insights for monitoring and evaluating the pandemic potential of field influenza viruses.
Efficacy of Combined Immunostimulation and Chemotherapy in Experimental Visceral Leishmaniasis (1983)

A regimen of combined immunostimulation and chemotherapy for the elimination of Leishmania donovani amastigotes was evaluated. An in vitro experimental model utilized cultured peritoneal macrophages from C57B1/6 mice infected with L. donovani tissue forms. Partial or complete activation of macrophages as judged by killing of tumor cells significantly enhanced the efficacy of sodium antimony gluconate (Pentostam). The quantity of drug required for elimination of parasites from immunostimulated cells was considerably lower than that required to achieve comparable amastigote killing in thioglycolate-elicited macrophages. In contrast, amphotericin B cleared infected cells of amastigotes at comparable drug levels when tested with immunostimulated and unstimulated macrophages. Several drugs tested inhibited the conversion of amastigotes to promastigotes in vitro but were ineffective in killing of intracellular tissue forms. Allopurinol and difluoromethylornithine (DMFO) blocked amastigote conversion significantly. These drugs at high concentrations, however, exerted only minimal toxicity for amastigotes residing within macrophages. Efficacy of combined therapy was also demonstrated in vivo. Immunoenhancement of L. donovani-infected mice with Corynebacterium parvum vaccine combined with a regimen of sodium antimony gluconate was significantly more effective than was immunotherapy or drug therapy alone.
Electrochromic device for the reversible electrodeposition system (2014)

A novel silver (Ag) deposition-based electrochromic device was developed for the reversible electrodeposition (RED) system. The electrochromic device can switch between transparent and mirror states in response to a change in the applied voltage. The dynamic range of the transmittance percent (%) for the fabricated device was about 90% at the 550 nm wavelength. A large-area RED display system was also successfully fabricated using the parted electrochromic cells of the honeycomb structure. The interelectrode space and the extent of the large-area RED display system were 50 μm and 10×10 cm, respectively.
Ultrasound in Radiology (2015)

During the past decade, ultrasound has expanded medical imaging well beyond the "traditional" radiology setting: a combination of portability, low cost, and ease of use makes ultrasound imaging an indispensable tool for radiologists as well as for other medical professionals who need to obtain imaging diagnosis or guide a therapeutic intervention quickly and efficiently. Ultrasound combines excellent ability for deep penetration into soft tissues with very good spatial resolution, with only a few exceptions (ie, those involving overlying bone or gas). Real-time imaging (up to hundreds and thousands of frames per second) enables guidance of therapeutic procedures and biopsies; characterization of the mechanical properties of the tissues greatly aids with the accuracy of the procedures. The ability of ultrasound to deposit energy locally brings about the potential for localized intervention encompassing the following: tissue ablation, enhancing penetration through the natural barriers to drug delivery in the body and triggering drug release from carrier microparticles and nanoparticles. The use of microbubble contrast agents brings the ability to monitor and quantify tissue perfusion, and microbubble targeting with ligand-decorated microbubbles brings the ability to obtain molecular biomarker information, that is, ultrasound molecular imaging. Overall, ultrasound has become the most widely used imaging modality in modern medicine; it will continue to grow and expand.
AdvancedMRTechniques for Preoperative Glioma Characterization: Part 2 (2023)

Preoperative clinical MRI protocols for gliomas, brain tumors with dismal outcomes due to their infiltrative properties, still rely on conventional structural MRI, which does not deliver information on tumor genotype and is limited in the delineation of diffuse gliomas. The GliMR COST action wants to raise awareness about the state of the art of advanced MRI techniques in gliomas and their possible clinical translation. This review describes current methods, limits, and applications of advanced MRI for the preoperative assessment of glioma, summarizing the level of clinical validation of different techniques. In this second part, we review magnetic resonance spectroscopy (MRS), chemical exchange saturation transfer (CEST), susceptibility-weighted imaging (SWI), MRI-PET, MR elastography (MRE), and MR-based radiomics applications. The first part of this review addresses dynamic susceptibility contrast (DSC) and dynamic contrast-enhanced (DCE) MRI, arterial spin labeling (ASL), diffusion-weighted MRI, vessel imaging, and magnetic resonance fingerprinting (MRF). EVIDENCE LEVEL: 3. TECHNICAL EFFICACY: Stage 2.