gebhart/patrepeval huggingface dataset:
Extracellular vesicles mediate the horizontal transfer of an active LINE‐1 retrotransposon (2019)

Long interspersed element-1 (LINE-1 or L1) retrotransposons replicate through a copy-and-paste mechanism using an RNA intermediate. However, little is known about the physical transmission of retrotransposon RNA between cells. To examine the horizontal transfer of an active human L1 retrotransposon mediated by extracellular vesicles (EVs), human cancer cells were transfected with an expression construct containing a retrotransposition-competent human L1 tagged with a reporter gene. Using this model, active retrotransposition events were detected by screening for the expression of the reporter gene inserted into the host genome by retrotransposition. EVs including exosomes and microvesicles were isolated from cells by differential centrifugation. The enrichment of L1-derived reporter RNA transcripts were detected in EVs isolated from cells expressing active L1 retrotransposition. The delivery of reporter RNA was confirmed in recipient cells, and reporter genes were detected in the genome of recipient cells. Additionally, employing qRT-PCR, we found that host-encoded factors are activated in response to increased exposure to L1-derived RNA transcripts in recipient cells. Our results suggest that the horizontal transfer of retrotransposons can occur through the incorporation of RNA intermediates delivered via EVs and may have important implications for the intercellular regulation of gene expression and gene function.
The Importance of Water for Purification of Longer Carbon Nanotubes for Nanocomposite Applications (2023)

Ultralong carbon nanotubes (UCNTs) are in high demand for nanocomposites applications due to their magnificent physical and chemical properties. UCNTs are synthesized by the catalytic chemical vapor deposition (CCVD) method and, before use as fillers in nanocomposites, should be purified of residual catalyst and non-CNT particles without significant destruction or scissoring of the UCNT. This study investigates the role of water vapor for purification of UCNTs from iron catalyst particles and the importance of water assistance in this process is confirmed. It was shown that wet air treatment of products of UCNTs CCVD synthesis under mild conditions can be used to sufficiently decrease residual iron catalyst content without significant carbon losses in comparison to the results obtained with dry air, while the residual iron content was shown to significantly influence the subsequent oxidation of different forms of carbons, including UCNTs. The increasing of D/G ratio of Raman spectra after wet air treatment of products of UCNTs CCVD synthesis makes it possible to conclude that iron catalyst particles transform into iron oxides and hydroxides that caused inner structural strains and destruction of carbon shells, improving removal of the catalyst particles by subsequent acid treatment. UCNTs purification with water assistance can be used to develop economically and ecologically friendly methods for obtaining fillers for nanocomposites of different applications.
Wavelength control and monitor for dense wavelength division multiplexing (DWDM) silicon photonic receiver (2023)

Techniques and circuitry for wavelength monitor and control are disclosed herein. The disclosed wavelength monitor and control circuitry and techniques are designed to realize a multi-channel DWDM optical link by using a photonic receiver that dynamically adjusts resonant wavelengths of the microring drop filter (MDF), as needed. The wavelength monitor and control circuitry can monitor and control the resonant wavelengths of multiple MDFs for a DWDM silicon photonics receiver with minimum power and area overhead. In an embodiment, circuitry for an optical receiver comprises an MDF having resonant wavelength for multiple DWDM channels, and circuitry to control and monitor the resonant wavelength of the MDF in real-time and in manner that compensates for deviation between actual resonant wavelength of the MDF and the incident optical wavelength of the MDF.
Unusually Severe Cases of Kingella kingae Osteoarticular Infections in Children (2013)

Because of their mild clinical features at onset, diagnosis of K. kingae osteoarticular infections can be delayed. Care should be taken for early detection and treatment of these infections because bony lytic lesions and potentially definitive growth cartilage damage can occur.
When Can We Use KinectFusion for Ground Truth Acquisition (2012)

Abstract — KinectFusion is a method for real-time capture of dense 3D geometry of the physical environment using a depth sensor. The system allows capture of a large dataset of 3D scene reconstructions at very low cost. In this paper we discuss the properties of the generated data and evaluate in which situations the method is accurate enough to provide ground truth models for low-level image processing tasks like stereo and optical flow estimation. The results suggest that the method is suitable for the fast acquisition of medium scale scenes (a few meters across), filling a gap between structured light and LiDAR scanners. For these scenes e.g. ground truth optical flow fields with accuracies of approximately 0.1 pixel can be created. We reveal an initial, high-quality dataset consisting of 57 scenes which can be used by researchers today, as well as a new, interactive tool implementing the KinectFusion method.
Schistosoma mansoni Venom Allergen Like Proteins Present Differential Allergic Responses in a Murine Model of Airway Inflammation (2012)

Our results suggest that members of the SmVAL family do present allergic properties; however, this varies significantly and therefore should be considered in the design of a schistosomiasis vaccine. Additionally, the murine model of airway inflammation proved to be useful in the investigation of allergic properties of potential vaccine candidates.
Toward lightweight biometric signal processing for wearable devices (2015)

Wearable devices are becoming a natural and economic means to gather biometric data from end users. The massive amount of information that they will provide, unimaginable until a few years ago, owns an immense potential for applications such as continuous monitoring for personalized healthcare and use within fitness applications. Wearables are however heavily constrained in terms of amount of memory, transmission capability and energy reserve. This calls for dedicated, lightweight but still effective algorithms for data management. This paper is centered around lossy data compression techniques, whose aim is to minimize the amount of information that is to be stored on their onboard memory and subsequently transmitted over wireless interfaces. Specifically, we analyze selected compression techniques for biometric signals, quantifying their complexity (energy consumption) and compression performance. Hence, we propose a new class of codebook-based (CB) compression algorithms, designed to be energy efficient, online and amenable to any type of signal exhibiting recurrent patterns. Finally, the performance of the selected and the new algorithm is assessed, underlining the advantages offered by CB schemes in terms of memory savings and classification algorithms.
Myoglobin Reconstituted with Ni Tetradehydrocorrin as a Methane‐Generating Model of Methyl‐coenzyme M Reductase (2019)

Abstract Myoglobin reconstituted with Ni tetradehydrocorrin was investigated as a model of F430‐containing methyl‐coenzyme M reductase, which catalyzes anaerobic methane generation. The Ni II tetradehydrocorrin complex has a Ni II /Ni I redox potential of −0.34 V vs. SHE and EPR spectroscopy indicates the formation of a Ni I species upon reduction by dithionite. This redox potential is approximately 0.31 V more positive than that of F430. The Ni I tetradehydrocorrin moiety is bound to the apo‐form of myoglobin to yield the reconstituted protein. Methane gas is generated in the reaction of the model with methyl iodide in the presence of the reconstituted protein under reductive conditions, whereas the Ni I complex itself does not produce methane gas. This is the first example of a protein‐based functional model of F430‐containing methyl‐coenzyme M reductase.
Effectiveness of delta-aminolevulinic acid-induced protoporphyrin as a photosensitizer for photodynamic therapy in vivo. (1995)

We examined the effectiveness of systemic administration of delta-aminolevulinic acid (delta-ALA) to induce endogenous protoporphyrin as a regimen for use in photodynamic therapy (PDT) of transplanted R3230AC rat mammary adenocarcinomas in vivo. Levels of porphyrins synthesized in various tissues after systemic administration of delta-ALA differed, with their accumulation in tumor tissue being dependent on both the dose and the time after delta-ALA administration. Tumor, liver, and intestine contained greater than 3.0 micrograms porphyrin/g tissue at 3 h after delta-ALA injection, whereas porphyrin levels in rat skin and muscle at that time were an order of magnitude lower. Analysis of tissue by HPLC revealed that the predominant porphyrin synthesized in tumors was protoporphyrin IX, whereas in liver, 18% of the total porphyrin detected was protoporphyrin IX, and in muscle, it was undetectable. Time-dependent studies of the uptake of 14C label from delta-ALA into the various tissues were not predictive of either the total amount of porphyrin or which porphyrin species would be present at 3 h after delta-ALA injection. Additionally, no simple relationship was apparent between the activities of certain selected enzymes involved in heme biosynthesis and the concentrations of porphyrins in the different tissues. High levels of tumor protoporphyrin IX were sustained by administration of two sequential doses of delta-ALA, at 3.0 and 1.5 h prior to irradiation. Using these treatment conditions, we inhibited R3230AC growth to an extent that was comparable to that obtained for Photofrin-induced PDT. High energy phosphate metabolism, measured by nuclear magnetic resonance spectroscopy in vivo, was dramatically impaired after delta-ALA-based PDT, with tumor ATP levels reduced to near zero by 4 h after irradiation. Our results demonstrated that delta-ALA-based PDT may be an alternative to current treatment protocols that use exogenously administered photosensitizers.
High power single lateral mode buried ridge laser with frustrated total internal reflection for spatial filtering (2003)

We demonstrate a spatial filter design that completely eliminates beam steering and oscillation of high order lateral modes in narrow stripe InGaAs single QW diode lasers.
Improved Butanol Production Using FASII Pathway in E. coli (2020)

<i>n</i>-Butanol is often considered a potential substitute for gasoline due to its physicochemical properties being closely related to those of gasoline. In this study, we extend our earlier work to convert endogenously producing butyrate via the FASII pathway using thioesterase TesBT to its corresponding alcohol, i.e., butanol. We first assembled pathway genes, i.e., <i>car</i> encoding carboxylic acid reductase from <i>Mycobacterium marinum</i>, <i>sfp</i> encoding phosphopantetheinyl transferase from <i>Bacillus subtilis</i>, and <i>adh2</i> encoding alcohol dehydrogenase from <i>S. cerevisiae</i>, responsible for bioconversion of butyrate to butanol in three different configurations (Operon, Pseudo-Operon, and Monocistronic) to achieve optimum expression of each gene and compared with the clostridial solventogenic pathway for <i>in vivo</i> conversion of butyrate to butanol under aerobic conditions. An <i>E. coli</i> strain harboring <i>car</i>, <i>sfp</i>, and <i>adh2</i> in pseudo-operon configuration was able to convert butyrate to butanol with 100% bioconversion efficiency when supplemented with 1 g/L of butyrate. Further, co-cultivation of an upstream strain (butyrate-producing) with a downstream strain (butyrate to butanol converting) at different inoculation ratios was investigated, and an optimized ratio of 1:4 (upstream strain: downstream strain) was found to produce ∼2 g/L butanol under fed-batch fermentation. Further, a mono-cultivation approach was applied by transforming a plasmid harboring <i>tesBT</i> gene into the downstream strain. This approach produced 0.42 g/L in a test tube and ∼2.9 g/L butanol under fed-batch fermentation. This is the first report where both mono- and co-cultivation approaches were tested and compared for butanol production, and butanol titers achieved using both strategies are the highest reported values in recombinant <i>E. coli</i> utilizing FASII pathway.
Stabilization of Tissue Specimens for Pathological Examination and Biomedical Research (2012)

Human tissue specimens are critical reagents in the diagnosis of disease and biomedical research. Tissues experience rapid degradation immediately after ligation from their blood supply. A variety of processing techniques are employed to prevent the degradation of tissue samples, principally chemical fixation and thermal processing. The success of processing techniques is measured by the preservation of tissue morphology, as well as the critical biomarkers. In preservation of tissue specimens, formaldehyde is the most widely used fixative that maintains tissue morphology. However, the cross-links resulting from chemical interactions between formaldehyde and biomolecules in the specimens introduce difficulties in detection and extraction of antigens for analysis. Alternative processing methods, such as chemical fixation (e.g., alcohol-based) or thermal processing (e.g., freezing) help avoid the loss of antigenicity due to cross-linking, but introduce morphological artifacts. In this article, we review methods of processing of fresh tissue samples, as well as the effects of these procedures on morphology and antigenicity of the preserved tissues as assessed by histology, immunohistochemistry, proteomics, and genomics.
Design characterization of microwave antenna BGA interconnect structure using test-validated physics-of-failure methods (2003)

A prototype two-component solder BGA interconnect structure was evaluated for attachment of microwave electronics to a phased array antenna element. The assembly comprised a dual circular polarization receiver module (DPR) for a direct broadcast satellite television (DBS) phased array antenna for mobile platforms. A fatigue life study was conducted to characterize the thermo-mechanical performance of a 42 I/O solder ball interconnect between a high temperature co-fired ceramic chip carrier and a plastic encapsulated metallic antenna probe. The BGA structure consisted of high temperature 90Pb10Sn solder balls with 63Sn37Pb attachment solder fillets. Alternative design configurations and material selections were evaluated for durability using concurrent design/analysis for rapid product development cycle times. A plastic-strain damage model based on a modified Coffin-Manson fatigue criterion was selected to represent the dominant BGA interconnect failure mechanism of low-cycle solder fatigue. Plastic-strain range characterization was completed using a nonlinear finite element code, Nike3d. Durability life was improved from 10s of thermal cycles to thousands with corresponding plastic-strain reductions at critical interconnects. The primary design change involved encapsulant CTE reduction. However, this change was not implemented in production due to inadequate dielectric loss performance with the replacement encapsulants. By using concurrent design/analysis, life-cycle durability characterization of a complex interconnect system was accomplished in a cost-efficient manner without time consuming experimental iterations.
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives (2009)

While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including humans. Infection results from environmental exposure to Coccidiodies, which is believed to grow as a soil saprophyte in arid deserts. To investigate hypotheses about the life history and evolution of Coccidioides, the genomes of several Onygenales, including C. immitis and C. posadasii; a close, nonpathogenic relative, Uncinocarpus reesii; and a more diverged pathogenic fungus, Histoplasma capsulatum, were sequenced and compared with those of 13 more distantly related Ascomycetes. This analysis identified increases and decreases in gene family size associated with a host/substrate shift from plants to animals in the Onygenales. In addition, comparison among Onygenales genomes revealed evolutionary changes in Coccidioides that may underlie its infectious phenotype, the identification of which may facilitate improved treatment and prevention of coccidioidomycosis. Overall, the results suggest that Coccidioides species are not soil saprophytes, but that they have evolved to remain associated with their dead animal hosts in soil, and that Coccidioides metabolism genes, membrane-related proteins, and putatively antigenic compounds have evolved in response to interaction with an animal host.
Femtosecond Generation of Nano-Fibers (2013)

A new approach to making extremely large aspect ratio glass nano-fibers with diameters typically 20 – 40 nm is described. The fabrication process utilizes a novel phenomenon occurring with the interaction of focused high power femtosecond laser radiation with transparent media.
Prevention of β Strand Movement into a Zymogen-like Position Does Not Confer Higher Activity to Coagulation Factor VIIa (2004)

Coagulation factor VIIa (FVIIa) belongs to the chymotrypsin family of S1 peptidases, whose members require the cleavage of at least one internal peptide bond to attain an active conformation. FVIIa also requires association with tissue factor (TF) to attain full catalytic competency. Without this, FVIIa has very low activity toward peptide and physiologic substrates. Reregistration of beta strands has been suggested to play a part in the activation of FVII, and their positioning is possibly important for the active conformation of FVIIa. To scrutinize this hypothesis, we have designed FVIIa variants which prevent beta strand movement and lock FVIIa in the alleged active conformation. The V299M mutation, alone or combined with the L280I mutation, was introduced to alter the first of two Leu-X-Val motifs in beta strand B2 and thereby prevent reregistration. Along the same line, C164V/V299C-FVIIa has a new disulfide which would keep beta strand B2 in the registration of active FVIIa. The amidolytic and proteolytic activities of V299M-, L280I/V299M-, and C164V/V299C-FVIIa were indistinguishable from or lower than those of wild-type FVIIa, and none of the mutants displayed an altered exposure of the N-terminal amino group of the protease domain. Moreover, the affinities of mutant and native FVIIa for TF increased to a similar extent upon incorporation of an active site inhibitor, and the enzymatic activities were equally stimulated by TF. In conclusion, we found no evidence that the mutants were in a more active state than native FVIIa. Thus, the proposed beta strand reregistration, if part of the regulatory mechanism governing FVIIa activity, apparently does not suffice for the transformation of FVIIa into an enzymatically active conformation. Our data raise the possibility that the structural differences between enzymatically latent (zymogen-like) and active FVIIa resemble those between trypsinogen and trypsin.
Pre-stresses due to trans-tibial socket donning: a nonlinear finite element analysis with contact (2003)

A finite element (FE) model of the trans-tibial residual limb and prosthetic socket was developed. The three-dimensional model accounts for shape differences between the socket and residual limb, and incorporates material nonlinearities. Contact, frictional slip, and separation at the limb-socket interface were permitted using automated contact without gap elements. FE estimates of interface stresses after socket donning compared favorably with experimental measurements, suggesting that the model may potentially contribute to improved understanding of interface biomechanics.
A novel communication role for CYP17A1 in the progression of castration‐resistant prostate cancer (2009)

CYP17A1 is a crucial enzyme for de novo androgen synthesis within the tumor microenvironment after removal of testicular androgens by castration. We provide evidence for a novel role for CYP17A1 in serum and further reiterate the importance of targeting this enzyme in CaP progression.
Gravitational acceleration of antiprotons and of positrons (1987)

Theories of quantum gravity predict the existence of spin-1 (graviphoton) and spin-0 (graviscalar) partners of the graviton, which will yield non-Newtonian, non-Einsteinian effects. In particular, although the static gravitational acceleration of matter to the Earth could be modified by small Yukawa-type terms, the static gravitational acceleration of antimatter would be modified by a larger factor. Since these new interactions couple to an unknown linear combination of baryon and lepton numbers, it is important to do both the planned antiproton gravity experiment and a proposed positron gravity experiment. Antihydrogen is also mentioned.
A report on the first year of the INitiative for the Evaluation of XML retrieval (INEX'02) (2004)

Abstract The INitiative for the Evaluation of XML retrieval (INEX) aims at providing an infrastructure to evaluate the effectiveness of content‐oriented XML retrieval systems. To this end, in the first round of INEX in 2002, a test collection of real world XML documents along with a set of topics and respective relevance assessments have been created with the collaboration of 36 participating organizations. In this article, we provide an overview of the first round of the INEX initiative.
The prognostic and predictive value of Tregs and tumor immune subtypes in postmenopausal, hormone receptor-positive breast cancer patients treated with adjuvant endocrine therapy: a Dutch TEAM study analysis (2015)

Evidence exists for an immunomodulatory effect of endocrine therapy in hormone receptor-positive (HR+ve) breast cancer (BC). Therefore, the aim of this study was to define the prognostic and predictive value of tumor immune markers and the tumor immune profile in HR+ve BC, treated with different endocrine treatment regimens. 2,596 Dutch TEAM patients were treated with 5 years of adjuvant hormonal treatment, randomly assigned to different regimens: 5 years of exemestane or sequential treatment (2.5 years of tamoxifen-2.5 years of exemestane). Immunohistochemistry was performed for HLA class I, HLA-E, HLA-G, and FoxP3. Tumor immune subtypes (IS) (low, intermediate & high immune susceptible) were determined by the effect size of mono-immune markers on relapse rate. Patients on sequential treatment with high level of tumor-infiltrating FoxP3+ cells had significant (p = 0.019, HR 0.729, 95% CI 0.560-0.949) better OS. Significant interaction for endocrine treatment and FoxP3+ presence was seen (OS p < 0.001). Tumor IS were only of prognostic value for the sequentially endocrine-treated patients (RFP: p = 0.035, HR intermediate IS 1.420, 95% CI 0.878-2.297; HR low IS 1.657, 95% CI 1.131-2.428; BCSS: p = 0.002, HR intermediate IS 2.486, 95% CI 1.375-4.495; HR low IS 2.422, 95% CI 1.439-4.076; and OS: p = 0.005, HR intermediate IS 1.509, 95% CI 0.950-2.395; HR low IS 1.848, 95% CI 1.277-2.675). Tregs and the tumor IS presented in this study harbor prognostic value for sequentially endocrine-treated HR+ve postmenopausal BC patients, but not for solely exemestane-treated patients. Therefore, these markers could be used as a clinical risk stratification tool to guide adjuvant treatment in this BC population.