gebhart/patrepeval huggingface dataset:
Gigahertz‐bandwidth optoelectronic differential amplifier (1988)

Abstract A wideband differential amplifier for electrical signals using modulated laser diodes and a novel optical receiver design shows better than 25‐dB common‐mode rejection ratio over a bandwidth of greater than 1 GHz.
Search for Higgs boson pair production in the $$ b\overline{b}W{W}^{*} $$ decay mode at $$ \sqrt{s} $$ = 13 TeV with the ATLAS detector (2019)

A bstract A search for Higgs boson pair production in the $$ b\overline{b}W{W}^{*} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>b</mml:mi> <mml:mover> <mml:mi>b</mml:mi> <mml:mo>¯</mml:mo> </mml:mover> <mml:mi>W</mml:mi> <mml:msup> <mml:mi>W</mml:mi> <mml:mo>*</mml:mo> </mml:msup> </mml:math> decay mode is performed in the $$ b\overline{b}\mathit{\ell \nu qq} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>b</mml:mi> <mml:mover> <mml:mi>b</mml:mi> <mml:mo>¯</mml:mo> </mml:mover> <mml:mi>ℓνqq</mml:mi> </mml:math> final state using 36.1 fb −1 of proton-proton collision data at a centre-of-mass energy of 13 TeV recorded with the ATLAS detector at the Large Hadron Collider. No evidence of events beyond the background expectation is found. Upper limits on the non-resonant pp → HH production cross section of 10 pb and on the resonant production cross section as a function of the HH invariant mass are obtained. Resonant production limits are set for scalar and spin-2 graviton hypotheses in the mass range 500 to 3000 GeV.
The Transcriptional Regulator Prdm1 Is Essential for the Early Development of the Sensory Whisker Follicle and Is Linked to the Beta-Catenin First Dermal Signal (2022)

<i>Prdm1</i> mutant mice are one of the rare mutant strains that do not develop whisker hair follicles while still displaying a pelage. Here, we show that <i>Prdm1</i> is expressed at the earliest stage of whisker development in clusters of mesenchymal cells before placode formation. Its conditional knockout in the murine soma leads to the loss of expression of <i>Bmp2</i>, <i>Shh</i>, <i>Bmp4</i>, <i>Krt17</i>, <i>Edar</i>, and <i>Gli1</i>, though leaving the β-catenin-driven first dermal signal intact. Furthermore, we show that <i>Prdm1</i> expressing cells not only act as a signaling center but also as a multipotent progenitor population contributing to the several lineages of the adult whisker. We confirm by genetic ablation experiments that the absence of macro vibrissae reverberates on the organization of nerve wiring in the mystacial pads and leads to the reorganization of the barrel cortex. We demonstrate that <i>Lef1</i> acts upstream of <i>Prdm1</i> and identify a primate-specific deletion of a <i>Lef1</i> enhancer named Leaf. This loss may have been significant in the evolutionary process, leading to the progressive defunctionalization and disappearance of vibrissae in primates.
The Intracellular Life ofCryptococcus neoformans (2013)

Cryptococcus neoformans is a fungal pathogen with worldwide distribution. Serological studies of human populations show a high prevalence of human infection, which rarely progresses to disease in immunocompetent hosts. However, decreased host immunity places individuals at high risk for cryptococcal disease. The disease can result from acute infection or reactivation of latent infection, in which yeasts within granulomas and host macrophages emerge to cause disease. In this review, we summarize what is known about the cellular recognition, ingestion, and killing of C. neoformans and discuss the unique and remarkable features of its intracellular life, including the proposed mechanisms for fungal persistence and killing in phagocytic cells.
Auxiliary Drive Systems for Aerial Devices (1980)

&lt;div class="htmlview paragraph"&gt;Significant advancements have been made in the development and application of more fuel efficient and cost effective auxiliary drive systems for powering aerial man lift equipment as used by the electric utility and telecommunications industries. Small gasoline powered engines and self-contained battery operated hydraulic systems not only reduce overall fuel consumption and contribute favorably to the ecological needs of the community, they reduce overall fuel and maintenance costs dramatically.&lt;/div&gt;
New syntheses of per‐N‐alkyl‐substituted triaza‐ and tetraaza‐crovm compounds containing an allyloxymethyl substituent (1989)

Abstract Seven new per‐ N ‐alkyl‐substituted triaza ‐ and tetraaza ‐crovm compounds have been prepared using commercially available or easily synthesized per‐ N ‐alkyl‐substituted oligoethylene and oligopropylene polyamines, tetraazapentaethylene and tetraazaheptaethylene glycols. Five of these new polyaza‐crowns have a pendant allyloxymethyl substituent.
Novel No-Wash Luminogenic Probes for the Detection of Transporter Uptake Activity (2015)

Luminogenic probes were designed and synthesized for the detection of uptake transporter activity in a lytic cell-based assay. These probes rely on a self-cleavable trimethyl lock quinone-cyanobenzothiazole (TMQ-CNBT) or trimethyl lock quinone-luciferin (TMQ-Luc) linked to the anion transporter substrate fluorescein. Upon cellular transport, the TMQ is reduced by viable cells, resulting in the facile intramolecular lactonization and rapid release of the bioluminescent reporter molecule. The uptake transporter activity can then be detected without removing and washing off the extracellular substrates. Six probes were tested with OATP1B1*1a and OATP1B3 overexpressing HEK293 cells, and all compounds showed up to 10.2-fold enhancement in uptake when compared to control cells. Uptake of TMQ-luciferin compounds 2, 4, and 6 increased linearly over time up to 30 min at a concentration ranging from 40 nM to 20 μM. The apparent Km values obtained at different time intervals up to 30 min were nearly identical for a given compound, which validates the 30 min window as appropriate for uptake transporter assays. The average apparent Km values ranged from 0.3 to 0.8 μM and 0.2 to 1.3 μM for OATP1B1*1a and OATP1B3, respectively, indicating good affinities to these anion transporters. Furthermore, uptake of compound 2 was inhibited by two inhibitors of OATP1B1*1a and OATP1B3: rifampicin and ritonavir. The preliminary results obtained from compound 2 exhibited a time-dependent, saturatable, and inhibitable nature of uptake, indicating the feasibility of using the probe for the detection of a transporter-mediated process. This add-and-read homogeneous assay may provide a convenient, rapid, and facile way to detect changes in transporter activity in a high-throughput format, and this assay design strategy could create a new platform for a general cell uptake assay for biomaterials in the future.
Quantification of energy loss mechanisms in organic light-emitting diodes (2010)

The external quantum efficiency of organic light-emitting diodes (OLEDs) is limited by several loss mechanisms. By applying a numerical model for the efficiency analysis of OLED devices, we analyze the distribution of the different energy loss mechanisms in bottom and top emission organic light-emitting diodes. We validate the findings by the comparison with experimental data measured on red state-of-the-art p-i-n devices containing the red phosphorescent emitting dye iridium(III)bis[2-methyldibenzo-(f, h)quinoxaline](acetylacetonate) [Ir(MDQ)2(acac)]. The model is used to design extremely efficient bottom and top emission diodes with 21% and 27% external quantum efficiencies, respectively.
A single point mutation activates the Moloney murine leukemia virus long terminal repeat in embryonal stem cells (1991)

The expression of Moloney murine leukemia virus (Mo-MuLV) and Mo-MuLV-derived vectors is restricted in undifferentiated mouse embryonal carcinoma and embryonal stem (ES) cells. We have previously described the isolation of retroviral mutants with host range properties expanded to embryonal cell lines. One of these mutants, the murine embryonic stem cell virus (MESV), is expressed in ES cell lines. Expression of MESV in these cells relies on DNA sequence motifs within the enhancer region of the viral long terminal repeat (LTR). Here we show that replacement of the Mo-MuLV enhancer region by sequences derived from the MESV LTR results in the activation of the Mo-MuLV LTR in ES cells. The enhancer regions of MESV and Mo-MuLV differ by seven point mutations. Of these, a single point mutation at position -166 is sufficient to activate the Mo-MuLV LTR and to confer enhancer-dependent expression to Mo-MuLV-derived retroviral vectors in ES cells. This point mutation creates a recognition site for a sequence-specific DNA-binding factor present in nuclear extracts of ES cells. This factor was found by functional assays to be the murine equivalent to human Sp1.
Cross‐species hybridization: Characterization of gene expression in woodchuck liver using human membrane arrays (2004)

Total RNA from normal adult woodchucks was analyzed using membrane arrays containing human cDNA clones, and the gene expression patterns were compared to human liver. Various hybridization and wash conditions were examined. In both the woodchuck and human livers, 352 genes were identified as highly expressed (Z-scores > or =1.96). These genes represented numerous liver functions: transcription, RNA processing, signal transduction, protein synthesis and degradation, as well as enzymes. Several genes were selected and expression was verified by Northern blots for woodchuck liver. There were no false positives but 29 genes were identified as false negatives, expressed only in human liver. Possible reasons for these false negatives were the length and percentage of homology between the two species, differences in the distribution and types of mismatches, and the sequence region spotted on the array. These were assessed by examining expression of the transferrin gene in both species. A 200-fold range of RNA concentration (0.1-20 microg total RNA) was also examined and the optimal RNA concentration was determined to be 5 microg. Membranes were capable of being hybridized and reprobed at least five times. The study demonstrates that cross-species hybridization is a valid method for identifying gene expression in woodchuck liver.
Solid-Phase Synthesis of 1,2-Diketones via Acetylene Oxidation: A Versatile Diversity Platform for the Combinatorial Synthesis of Heterocycles (2010)

Investigations towards the solid-phase synthesis of 1,2-diketones via the oxidation of acetylenes and their use in the combinatorial synthesis of heterocycles such as imidazoles and quin­oxalines are described.
Patient Reported Pain and Disability Following a Distal Radius Fracture: A Prospective Study (2017)

The majority of people that are experiencing no or low patient reported pain and disability one year following a DRF can expect to retain their positive outcome 10-20 years later. This study did not identify how to predict worsened outcome.
Optical properties of organic semiconductors (2020)

Abstract Organic semiconductors are often called excitonic materials since their optical properties derive from the photogeneration of excitons, that is, bound electron–hole pairs. Organic excitons are either Frenkel or charge-transfer-like with binding energies of 0.5–1.0 eV, making them stable at room temperature. This chapter describes the fundamental optical properties of organics, starting with those of individual molecules, and then building the solid from pairs of molecules (dimers) and oligomers. Theoretical approaches to describe optical properties start by introducing the Born–Oppenheimer approximation and the Franck–Condon principle. Calculational approaches to understanding optical characteristics based on the linear combination of atomic orbitals are described. Both theory and experimental observation of optical phenomena are discussed in detail. Also, electron spin, spin–orbit coupling, fluorescence, and phosphorescence are quantitatively described. Finally, long and short range energy transfer, exciton diffusion, and annihilation processes ae described.
Adaptation of Methanogenic Communities to the Cofermentation of Cattle Excreta and Olive Mill Wastes at 37°C and 55°C (2010)

The acclimatization of methanogens to two-phase olive mill wastes (TPOMW) was investigated in pilot fermenters started up with cattle excreta (37°C) and after changing their feed to excreta plus TPOMW (37°C or 55°C) or TPOMW alone (37°C) until a steady state was reached (28 days). Methanogenic diversity was screened using a phylogenetic microarray (AnaeroChip), and positive targets were quantified by real-time PCR. Results revealed high phylogenetic richness, with representatives of three out of the four taxonomic orders found in digesters. Methanosarcina dominated in the starting excreta (>96% of total 16S rRNA gene copies; over 45 times more abundant than any other methanogen) at high acetate (0.21 g liter(-1)) and ammonia N concentrations (1.3 g liter(-1)). Codigestion at 37°C induced a 6-fold increase of Methanosarcina numbers, correlated with CH(4) production (r(Pearson) = 0.94; P = 0.02). At 55°C, the rise in temperature and H(2) partial pressure induced a burst of Methanobacterium, Methanoculleus, Methanothermobacter, and a group of uncultured archaea. The digestion of excreta alone resulted in low but constant biogas production despite certain oscillations in the methanogenic biomass. Unsuccessful digestion of TPOMW alone was attributed to high Cu levels inducing inhibition of methanogenic activity. In conclusion, the versatile Methanosarcina immediately adapted to the shift from excreta to excreta plus TPOMW and was responsible for the stimulated CH(4) production at 37°C. Higher temperatures (55°C) fostered methanogenic diversity by promoting some H(2) scavengers while yielding the highest CH(4) production. Further testing is needed to find out whether there is a link between increased methanogenic diversity and reactor productivity.
Relationship Between Low Bone Mineral Density and Fractures With Incident Cardiovascular Disease: A Systematic Review and Meta-Analysis (2017)

An increasing evidence base suggests that low bone mineral density (BMD) and fractures are associated with cardiovascular disease (CVD). We conducted a systematic review and meta-analysis summarizing the evidence of low BMD and fractures as risk factors for future CVD. Two independent authors searched major databases from inception to August 1, 2016, for longitudinal studies reporting data on CVD incidence (overall and specific CVD) and BMD status and fractures. The association between low BMD, fractures, and CVD across longitudinal studies was explored by calculating pooled adjusted hazard ratios (HRs) ±95% confidence intervals (CIs) with a random-effects meta-analysis. Twenty-eight studies (18 regarding BMD and 10 fractures) followed a total of 1,107,885 participants for a median of 5 years. Taking those with higher BMD as the reference, people with low BMD were at increased risk of developing CVD during follow-up (11 studies; HR = 1.33; 95%CI, 1.27 to 1.38; I<sup>2</sup> = 53%), after adjusting for a median of eight confounders. This finding was confirmed using a decrease in one standard deviation of baseline BMD (9 studies; HR = 1.16; 95% CI, 1.09 to 1.24; I<sup>2</sup> = 69%). The presence of fractures at baseline was associated with an increased risk of developing CVD (HR = 1.20; 95% CI, 1.06 to 1.37; I<sup>2</sup> = 91%). Regarding specific CVDs, low BMD was associated with an increased risk of developing coronary artery disease, cerebrovascular conditions, and CVD-associated death. Fractures at baseline was associated with an increased risk of cerebrovascular conditions and death due to CVD. In conclusion, low BMD and fractures are associated with a small, but significant increased risk of CVD risk and possibly death. © 2017 American Society for Bone and Mineral Research.
Figure S3 from High <i>FGFR1–4</i> mRNA Expression Levels Correlate with Response to Selective FGFR Inhibitors in Breast Cancer (2023)

&lt;p&gt;Supplementary Figure 3. FGFR1-4 and FGF3/4/19 CN and mRNA levels in BC. A) Proportion of BCs harboring FGFR1-4 amplification in five cohorts of primary (TCGA, METABRIC and MSK) or metastatic tumors (INSERM and The Metastatic Breast Cancer Project). Data was acquired from cBioPortal (cbioportal.org/datasets). B) Correlation analysis between FGFR1-4 CN and mRNA levels in the TCGA BC cohort. Pearson correlation coefficient (r2) is shown. C) and D) FGFR1 and 11q13 (FGF3/4/19 and CCND1) CN co-amplification analysis in the VHIO and TCGA BC cohorts, respectively. Red bars denote cases with 11q13 amplification and blue bars FGFR1 amplification. Statistical test: Fisher's exact test. E) and F) FGFR1 and FGF mRNA co-expression analysis in the VHIO and TCGA BC cohorts, respectively. Statistical test: Sidak's multiple comparisons test.&lt;/p&gt;
Groups IV, V, and X Phospholipases A2s in Human Neutrophils (2002)

The bacterial tripeptide formyl-Met-Leu-Phe (fMLP) induces the secretion of enzyme(s) with phospholipase A(2) (PLA(2)) activity from human neutrophils. We show that circulating human neutrophils express groups V and X sPLA(2) (GV and GX sPLA(2)) mRNA and contain GV and GX sPLA(2) proteins, whereas GIB, GIIA, GIID, GIIE, GIIF, GIII, and GXII sPLA(2)s are undetectable. GV sPLA(2) is a component of both azurophilic and specific granules, whereas GX sPLA(2) is confined to azurophilic granules. Exposure to fMLP or opsonized zymosan results in the release of GV but not GX sPLA(2) and most, if not all, of the PLA(2) activity in the extracellular fluid of fMLP-stimulated neutrophils is due to GV sPLA(2). GV sPLA(2) does not contribute to fMLP-stimulated leukotriene B(4) production but may support the anti-bacterial properties of the neutrophil, because 10-100 ng per ml concentrations of this enzyme lead to Gram-negative bacterial membrane phospholipid hydrolysis in the presence of human serum. By use of a recently described and specific inhibitor of cytosolic PLA(2)-alpha (group IV PLA(2)alpha), we show that this enzyme produces virtually all of the arachidonic acid used for the biosynthesis of leukotriene B(4) in fMLP- and opsonized zymosan-stimulated neutrophils, the major eicosanoid produced by these pro-inflammatory cells.
Feature learning based on visual similarity triplets in medical image analysis: A case study of emphysema in chest CT scans (2018)

Supervised feature learning using convolutional neural networks (CNNs) can provide concise and disease relevant representations of medical images. However, training CNNs requires annotated image data. Annotating medical images can be a time-consuming task and even expert annotations are subject to substantial inter- and intra-rater variability. Assessing visual similarity of images instead of indicating specific pathologies or estimating disease severity could allow non-experts to participate, help uncover new patterns, and possibly reduce rater variability. We consider the task of assessing emphysema extent in chest CT scans. We derive visual similarity triplets from visually assessed emphysema extent and learn a low dimensional embedding using CNNs. We evaluate the networks on 973 images, and show that the CNNs can learn disease relevant feature representations from derived similarity triplets. To our knowledge this is the first medical image application where similarity triplets has been used to learn a feature representation that can be used for embedding unseen test images
A novel combination of chemotherapy and immunotherapy controls tumor growth in mice with a human immune system (2019)

Mice reconstituted with a human immune system and bearing human tumors represent a promising model for developing novel cancer immunotherapies. Here, we used mass cytometry and multi-parametric flow cytometry to characterize human leukocytes infiltrating a human breast cancer tumor model in immunocompromised NOD.SCID.γc-null mice reconstituted with a human immune system and compared it to samples of breast cancer patients. We observed highly activated human CD4<sup>+</sup> and CD8<sup>+</sup> T cells in the tumor, as well as minor subsets of innate immune cells in both settings. We also report that ICOS<sup>+</sup> CD4<sup>+</sup> regulatory T cells (Treg) were enriched in the tumor relative to the periphery in humanized mice and patients, providing a target to affect Treg and tumor growth. Indeed, administration of a neutralizing mAb to human ICOS reduced Treg proportions and numbers and improved CD4 + T cell proliferation in humanized mice. Moreover, a combination of the anti-ICOS mAb with cyclophosphamide reduced tumor growth, and that was associated with an improved CD8 to Treg ratio. Depletion of human CD8<sup>+</sup> T cells or of murine myeloid cells marginally affected the effect of the combination therapy. Altogether, our results indicate that a combination of anti-ICOS mAb and chemotherapy controls tumor growth in humanized mice, opening new perspectives for the treatment of breast cancer. One sentence summary: Targeting ICOS in combination with chemotherapy is a promising strategy to improve tumor immunity in humans.
CT-Deployed Hydrajet Perforating in Horizontal Completions Provides New Approaches to Multistage Hydraulic Fracturing Applications (2006)

The application of horizontal completions in lower-permeability formations is continuing to proliferate on a global scale. Caused either by formation damage issues or the very heterogeneous nature of many such reservoirs, actual wells will underperform when compared to original predictions from reservoir simulations. This will continue to result in a need for effective hydraulic-fracturing stimulations for many of these wells to reach economic production levels. Horizontal completions in moderate- to low-permeability reservoirs present the challenge of cost constraints that seldom allow the use of long-proven methods such as cemented completions and individual-fracturing of numerous zones with bridge plug isolation and multiple perforating runs. Some new methods being applied to overcome this problem require expensive downhole
Volcano plot comparing the <i>hva1Δ</i> and H99W strains. (2016)

&lt;p&gt;Metabolites that are elevated in the &lt;i&gt;hva1Δ&lt;/i&gt; strain versus H99W are red, while those that are decreased in the &lt;i&gt;hva1Δ&lt;/i&gt; strain versus H99W are blue. To be colored the fold change must be greater than 1.5 and p-value&lt;0.05. These data are suggestive of a block in the in the production of 2-ketoglutarate in the &lt;i&gt;hva1Δ&lt;/i&gt; strain compared to H99W.&lt;/p&gt;