gebhart/patrepeval huggingface dataset:
Recurrent genetic abnormalities in human pluripotent stem cells: definition and routine detection in culture supernatant by targeted droplet digital PCR (2019)

Summary Genomic integrity of human pluripotent stem cells (hPSCs) is essential for research and clinical applications. However, genetic abnormalities can accumulate during hPSC generation and routine culture and following gene editing. Their occurrence should be routinely monitored, but the current assays to assess hPSC genomic integrity are not fully suitable for suchregular screening. To address this issue, we first carried out a large meta-analysis of all hPSC genetic abnormalities reported in more than 100 publications and identified 738 recurrent genetic abnormalities (i.e., overlapping abnormalities found in at least five distinct scientific publications). We then developed a test based on the droplet digital PCR technology that can potentially detect 94.3% of these hPSC recurrent genetic abnormalities in DNA extracted from culture supernatant samples. This test can be used to routinely screen genomic integrity in hPSCs.
FAIR Principles: Interpretations and Implementation Considerations (2019)

The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 FAIR guiding principles do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability and Reusability of digital resources. This has likely contributed to the broad adoption of the FAIR principles, because individual stakeholder communities can implement their own FAIR solutions. However, it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations. Thus, while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways, for true interoperability we need to support convergence in implementation choices that are widely accessible and (re)-usable. We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible, robust, widespread and consistent FAIR implementations. Any self-identified stakeholder community may either choose to reuse solutions from existing implementations, or when they spot a gap, accept the challenge to create the needed solution, which, ideally, can be used again by other communities in the future. Here, we provide interpretations and implementation considerations (choices and challenges) for each FAIR principle.
Personnel Dosimetry Using Thermoluminescent Dosimeters (1968)

A routine system of personnel dosimetry utilizing the phenomena of thermoluminescence has been developed at the National Reactor Testing Station (NRTS). Research in thermoluminescent application techniques was initiated in early 1965 with the hope of developing a suitable system for long-term monitoring of personnel exposed to near background levels of radiation. The dosimeter utilizes two lithium fluoride-teflon disc dosimeters that are held in a plastic dosimeter retainer that is the same size and shape as a standard film packet. The dosimeters are positioned in the open window area and the cadmium filter area of the NRTS badge. An insert in the plastic retainer contains a punched binary code for identification. The experimental results are discussed in terms of reliability, reproducibility, response characteristics, and other factors that affect the validity of performance. The initial field experience of the system since its application in November 1966 is presented.
Tumor necrosis factor-alpha modulates the expression of its p60 receptor and several cytokines in rat tracheal epithelial cells (1996)

The epithelium of the conducting airways is frequently the target of toxic chemical and microbial agents causing inflammation, hypersecretion, and epithelial necrosis. TNF-alpha is a prototypical inflammatory cytokine released by macrophages and other inflammatory cells. The purpose of this study was to characterize TNF-alpha receptors in fully differentiated rat tracheal epithelial (RTE) cells in culture and to examine the effects of TNF-alpha on this epithelium. We demonstrated the presence of approximately 250 TNF-alpha receptors per RTE cell. Both known receptor types, p60 (TNF-RI, CD 120a) and p80 (TNF-RII, CD 120b), were expressed. The level of p80 mRNA was unaffected by TNF-alpha treatment, whereas p60 mRNA was down-regulated, and soluble TNF-RI was shed from cells within 30 min. Treatment of RTE cultures with TNF-alpha (1000 U) caused no cytotoxicity (as determined by lactate dehydrogenase release). However, TNF-alpha exposure of the cultures induced the expression of several inflammatory mediators, as determined by reverse transcription-PCR and ELISA. Low levels of IFN-gamma mRNA became detectable after 4 h. Increased levels of TNF-alpha mRNA and protein were found, which peaked after 6 h of TNF-alpha treatment, but neither IL-1 alpha nor IL-1 beta was detectable. Calcium-independent nitric oxide synthase transcripts were elevated two- to threefold within 2 to 6 h of TNF-alpha treatment. These findings suggest that the airway epithelium may actively participate in the pathogenesis of airway inflammation through the production of mediators similar to those found in a Th1 response.
High-Speed Visible Light Communications Using Multiple-Resonant Equalization (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> White light-emitting diodes (LEDs) are becoming widespread in commercial lighting applications, and there are predictions that they will be in common use in domestic applications in the future. There is also growing interest in using these devices for both illumination and communications. One of the major challenges in visible light communications is the low modulation bandwidth (BW) available from devices, which is typically several megahertz. In this letter, we describe a link that uses 16 LEDs which are modulated using a resonant driving technique, creating an overall BW of 25 MHz. This is used to implement a 40-Mb/s nonreturn-to-zero <emphasis emphasistype="smcaps">on–off</emphasis> keying link which operates at low error rates, and also provides illumination at levels sufficient for a standard office environment. </para>
Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors (2008)

This paper provides comprehensive analysis and characterization of Pot II family, and enlightens our understanding on the strategies (Gene and domain duplication, structural circular permutation and molecular adaptation) of Solanaceae plants for defending pathogenic attacks through the evolution of Pot II genes.
<title>Thin film multilayers of TiNi/TiO<formula><inf><roman>2</roman></inf></formula>/PZT: mechanical and ferroelectrical characterization</title> (1994)

This paper concerns the mechanical and ferroelectrical properties of TiNi/TiO<SUB>2</SUB>/PZT multilayers. As prototypes for `smart' materials, the TiNi and oxide ceramics must be capable of both sensing and actuation functions. For testing of the properties of these meso-scale structures to occur, the mechanical and electrical properties of the individual components need to be characterized. The mechanical properties of the PZT thin film were characterized by Scanning Electron Microscopy and optical microscopy. Cracking and defects in the PZT were observed for thick films, however thin PZT films of 1 micron or less showed better mechanical integrity. The ferroelectric properties of the PZT thin films were smaller than for bulk PZT; this was likely associated with leakage currents caused by the mechanical imperfections of the films.
Channel Data Retrieval in Page-Based Holographic Data Storage (2006)

A channel data retrieval scheme for page-based holographic data storage has been developed. It includes several signal-processing blocks for retrieving data reliably under noisy condition, namely, a frame grabber for capturing data adaptively in a rotating disk, a mark detector for tracing the data location, an equalizer for compensating interference, a two-dimensional modulation decoder for suppressing errors, and a three-dimensional error correction decoder for correcting errors generated by the holographic storage channel. The proposed scheme has been implemented with a field-programmable gate array chip and applied to actual data retrieval from holographic data storage. With the proposed channel data retrieval hardware, the user video data is successfully reconstructed from the holographic disk, which contains video data as holograms.
<sup>15</sup>N NMR Investigation of the Covalent Binding of Reduced TNT Amines to Soil Humic Acid, Model Compounds, and Lignocellulose (2002)

The five major reductive degradation products of TNT-4ADNT (4-amino-2,6-dinitrotoluene), 2ADNT (2-amino-4,6-dinitrotoluene), 2,4DANT (2,4-diamino-6-nitrotoluene), 2,6DANT (2,6-diamino-4-nitrotoluene), and TAT (2,4,6-triaminotoluene)-labeled with 15N in the amine positions, were reacted with the IHSS soil humic acid and analyzed by 15N NMR spectrometry. In the absence of catalysts, all five amines underwent nucleophilic addition reactions with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and nonheterocyclic condensation products. Imine formation via 1,2-addition of the amines to quinone groups in the soil humic acid was significant with the diamines and TAT but not the monoamines. Horseradish peroxidase (HRP) catalyzed an increase in the incorporation of all five amines into the humic acid. In the case of the diamines and TAT, HRP also shifted the binding away from heterocyclic condensation product toward imine formation. A comparison of quantitative liquid phase with solid-state CP/MAS 15N NMR indicated that the CP experiment underestimated imine and heterocyclic nitrogens in humic acid, even with contact times optimal for observation of these nitrogens. Covalent binding of the mono- and diamines to 4-methylcatechol, the HRP catalyzed condensation of 4ADNT and 2,4DANT to coniferyl alcohol, and the binding of 2,4DANT to lignocellulose with and without birnessite were also examined.
Melan-A, A New Melanocytic Differentiation Marker (1999)

Melan-A/MART-1 is a recently identified new melanocytic differentiation marker, which is recognized as an antigen on melanoma cells by cytotoxic T-lymphocytes. It is of interest for clinicians as potential immunotherapeutic target and it is relevant for pathologists as a novel diagnostic marker, since two antibodies (A103 and M2-7C10) have become available to study Melan-A/MART-1 expression on archival material. Both antibodies are useful in the differential diagnosis of melanocytic tumors, especially metastatic tumors, since they are more sensitive than HMB-45. Both antibodies are also of diagnostic value in the recognition of perivascular epithelioid cell tumors (angiomyolipoma, lymphangioleiomyomatosis, and clear cell tumor). Since A103 has the unique property of staining many steroid hormone producing cells, this antibody is also of value for the recognition of tumors derived from these cells, such as adrenocortical carcinomas. Both antibodies are likely to be included in the routine diagnostic armamentarium of many immunohistochemical laboratories in the near future.
Training Deep Learning Based Image Denoisers From Undersampled Measurements Without Ground Truth and Without Image Prior (2019)

Compressive sensing is a method to recover the original image from undersampled measurements. In order to overcome the ill-posedness of this inverse problem, image priors are used such as sparsity, minimal total-variation, or self-similarity of images. Recently, deep learning based compressive image recovery methods have been proposed and have yielded state-of-the-art performances. They used data-driven approaches instead of hand-crafted image priors to regularize ill-posed inverse problems with undersampled data. Ironically, training deep neural networks (DNNs) for them requires "clean" ground truth images, but obtaining the best quality images from undersampled data requires well-trained DNNs. To resolve this dilemma, we propose novel methods based on two well-grounded theories: denoiser-approximate message passing (D-AMP) and Stein's unbiased risk estimator (SURE). Our proposed methods were able to train deep learning based image denoisers from undersampled measurements without ground truth images and without additional image priors, and to recover images with state-of-the-art qualities from undersampled data. We evaluated our methods for various compressive sensing recovery problems with Gaussian random, coded diffraction pattern, and compressive sensing MRI measurement matrices. Our proposed methods yielded state-of-the-art performances for all cases without ground truth images. Our methods also yielded comparable performances to the methods with ground truth data.
Granulocyte Colony-Stimulating Factor-Producing Large Cell Undifferentiated Carcinoma of the Lung. (1992)

We report a case of granulocyte colony-stimulating factor (G-CSF) producing lung cancer. A 38-year-old Japanese woman had a large cell undifferentiated carcinoma of the left lung with severe granulocytosis without any evidence of infection. A specimen was taken from a metastatic cervical lymph node and a tumor cell line was established. The culture supernatant of the line as well as patient's serum exhibited a high level of G-CSF by sandwich enzyme immunoassay. Immunohistochemical analysis demonstrated that tumor cells from transplanted nude mice were stained granularly in the cytoplasma by anti-human G-CSF monoclonal antibody, 4A6.
Epidermal Dendritic Cell Populations in the Flaky Skin Mutant Mouse (1993)

Flaky skin (gene symbol: fsn) is an autosomal recessive mouse mutation that causes pathologic changes in the skin yielding a papulosquamous disease resembling human psoriasis. Preliminary studies of epidermal sheets from foot pads of fsn/fsn mice stained for Ia+ Langerhans cells (LC) or Thy-1+ dendritic epidermal cells (Thy-1+ DEC) indicated a rise in LC numbers at the time of weaning, when the skin lesion becomes clinically evident. To further investigate this observation, epidermal sheets were obtained from the ear, dorsal skin, and foot pads from replicates of 6 female mice (both mutants and normal littermates) on weekly intervals from birth to 8 weeks of age. Dorsal skin epidermal thickness was quantitated by computer assisted image analysis and found to be significantly thickened from one week onward in the mutant mice. Using immunofluorescence microscopy, epidermal dendritic cell numbers were determined following staining with antibodies for the following markers: Ia, NLDC-145, and S-100 (for LC) or Thy 1.2 and asialo-GM1 (for Thy-1+ DEC). Use of all 5 markers to evaluate skin from 3 different locations yielded a subtle but significant increase in LC and Thy-1+ DEC in flaky skin mice. Of the three sites evaluated, the dorsal skin and ear epidermal sheets were most informative, which corresponded to the degree of pathological involvement. Mice doubly homozygous for fsn and for the severe combined immunodeficiency (scid) mutation developed the psoriasiform dermatitis. Bone marrow grafts from fsn/fsn homozygotes to homozygous scid/scid mice reproduce the skin lesion. These studies suggest that the psoriasiform dermatitis in the flaky skin mouse mutation is associated with abnormalities at the level of hematopoietic progenitor cells.
A stretchable and transparent SWNT strain sensor encapsulated in thin PDMS films (2013)

In this paper, a stretchable and transparent strain sensor made of an ultrathin film of single-walled carbon nanotubes (SWNTs) encapsulated inside poly(dimethyl siloxane) (PDMS) films is presented. A surface plasma treatment, followed by a solution based, low temperature drop casting process was developed and utilized to fabricate the strain sensor. The fabricated SWNTs strain sensor functions as a two-terminal resistor which changes its resistance when the sensor is stretched. The strain sensor was tested with 10% tensile cyclic strain and was found to handle strains of up to 35%. With PDMS encapsulation, the effect of environmental gases to the response of the SWNT strain sensors was eliminated. The electrical response of the SWNT strain sensor was highly reversible and repeatable after the initial conditioning step. The reliability of this sensor was evaluated up to 200 cycles at 4% strain. Our results demonstrate the possibility of using ultrathin SWNT films as a stretchable, transparent and reliable strain sensor.
Radiation Dosimetry in <sup>177</sup>Lu-PSMA-617 Therapy Using a Single Posttreatment SPECT/CT Scan: A Novel Methodology to Generate Time- and Tissue-Specific Dose Factors (2019)

Calculation of radiation dosimetry in targeted nuclear medicine therapies is traditionally resource-intensive, requiring multiple posttherapy SPECT acquisitions. An alternative approach is to take advantage of existing pharmacokinetic data from these smaller cohorts to enable dose computation from a single posttreatment scan in a manner that may be applied to a much broader patient population. <b>Methods:</b> In this work, a technical description of simplified dose estimation is presented and applied to the assessment of <sup>177</sup>Lu-prostate-specific membrane antigen (PSMA)-617 therapy for metastatic prostate cancer. By normalizing existing time-activity curves to a single measurement time, it is possible to calculate a mean and range of time-integrated activity values that relate to absorbed radiation dose. To assist with accurate pharmacokinetic modeling of the training cohort, a method for contour-guided image registration was developed. <b>Results:</b> Tissue-specific dose conversion factors for common posttreatment imaging times are reported along with a characterization of added uncertainty in comparison to a traditional serial imaging protocol. Single-time-point dose factors for tumor were determined to be 11.0, 12.1, 13.6, and 15.2 Gy per MBq/mL at image times of 24, 48, 72, and 96 h, respectively. For normal tissues, parotid gland factors were 6.7, 9.4, 13.3, and 19.3 Gy per MBq/mL at those times, and kidneys were 7.1, 10.3, 15.0, and 22.0 Gy per MBq/mL. Tumor dose estimates were most accurate using delayed scanning at times beyond 72 h. Dose to healthy tissues is best characterized by scanning patients in the first 2 d of treatment because of the larger degree of tracer clearance in this early phase. <b>Conclusion:</b> This work demonstrates a means for efficient dose estimation in <sup>177</sup>Lu-PSMA-617 therapy. By providing methods to simplify and potentially automate radiation dosimetry, we hope to accelerate the understanding of radiobiology and development of dose-response models in this unique therapeutic context.
Relay Techniques for MIMO Wireless Networks with Multiple Source and Destination Pairs (2006)

A multiple-input multiple-output (MIMO) relay network comprises source, relay, and destination nodes, each of which is equipped with multiple antennas. In a previous work, we proposed a MIMO relay scheme for a relay network with a single source and destination pair in which each of the multiple relay nodes performs QR decompositions of the backward and forward channel matrices in conjunction with phase control (QR-P-QR). In this paper, we extend this scheme to a MIMO relay network employing multiple source and destination pairs. Towards this goal, we use a group nulling approach to decompose a multiple S-D MIMO relay channel into parallel independent S-D MIMO relay channels, and then apply the QR-P-QR scheme to each of the decomposed MIMO relay links. We analytically show the logarithmic capacity scaling of the proposed relay scheme. Numerical examples confirm that the proposed relay scheme offers higher capacity than existing relay schemes.
Decarbonylation of Aliphatic Aldehydes by a Tp<sup>Me2</sup>Ir(III) Metallacyclopentadiene (2012)

The Ir(III) compound TpMe2Ir[C(CO2Me)═C(CO2Me)C(CO2Me)═C(CO2Me)](OH2) (1) reacts thermally with aliphatic aldehydes RC(O)H (R = Me, tBu) to lead to the decarbonylation products TpMe2Ir[C(CO2Me)═C(CO2Me)C(CO2Me)═C(CO2Me)](CO) (2) and RH. In turn, formaldehyde reacts with 1, yielding a product resulting from the hydrogenation of one of the double bonds of the iridacycle. Theoretical calculations reveal the role of the metallacycle as a shuttle for the transfer of the aldehyde H atom. Under photochemical (UV) irradiation, the decarbonylation reaction becomes catalytic for a variety of aliphatic aldehydes.
New agents for<i>Clostridium difficile</i>-associated disease (2008)

The new antibiotics in development and preclinical development reflect next-generation versions of older drugs or two new mechanism-of-action class drugs (OPT-80, REP3123). Based on the current preclinical and clinical data, the next-generation drugs impart only a subtle difference from the intrinsic weaknesses of their genre. In contrast, OPT-80 and REP3123 seem to be differentiated.
Solid-immersion fluorescence microscopy with increased emission and super resolution (2015)

We investigate solid-immersion fluorescence microscopy suitable for super-resolution nanotechnology and biological imaging, and have observed limit of resolution as small as 15 nm with microspheres, mitochondria, and chromatin fibers. We have further observed that fluorescence efficiency increases with excitation power density, implicating appreciable stimulated emission and increased resolution. We discuss potential advantages of the solid-immersion microscopy, including combined use with previously established super-resolution techniques for reaching deeper beyond the conventional diffraction limit.
Piece wise linear least–squares approximation of planar curves (1990)

Two algorithms for solving the piecewise linear least–squares approximation problem of plane curves are presented. The first is for the case when the L 2 residual (error) norm in any segment is not to exceed a pre–assigned value. The second algorithm is for the case when the number of segments is given and a (balanced) L 2 residual norm solution is required. The given curve is first digitized and either algorithm is then applied to the discrete points. For each segment, we obtain the upper triangular matrix R in the QR factorization of the (augmented) coefficient matrix of the resulting system of linear equations. The least–squares solutions are calculated in terms of the R (and Q) matrices. The algorithms then work in an iterative manner by updating the least–squares solutions for the segments via up dating the R matrices. The calculation requires as little computational effort as possible. Numerical results and comments are given. This, in a way, is a tutorial paper.
Spectra of Free Oscillations from an Aftershock Sequence (1967)

The question arises as to whether the spectrum of oscillations generated by a main shock and its aftershock sequence differs from that of a single event. It is shown that a formal difference occurs if the probability of the occurrence of an aftershock and its magnitude are functions of time. When applied to an actual aftershock sequence, the discrepancy in frequency of the spectral peak is probably less than 0·01 minutes, although some skewing in the shape of the spectrum may occur.