gebhart/patrepeval huggingface dataset:
Role of bcl-2 in the Development of Lymphoid Cells From the Hematopoietic Stem Cell (1997)

To investigate the role of bcl-2 in lymphohematopoiesis, a long-term bone marrow reconstitution system was established. Transplantation of 1,000 c-Kit+ Sca-1+ and lineage markers negative cells from bcl-2-l-mouse bone marrow resulted in long-term reconstitution of nonlymphoid cells. However, T cells were totally absent and B-lymphocyte development was severely impaired at a very early stage of differentiation in the chimeric mouse. On the other hand, transplantation of day 14 fetal liver cells from bcl-2-l-mice resulted in generation of both T and B cells in the recipient, albeit transiently. These data suggest that bcl-2 plays a critical role in the development of lymphoid progenitor cells from the hematopoietic stem cell (HSC), but is not essential for the development of nonlymphoid cells and the self-renewal of HSC. In addition, lymphopoiesis from fetal liver HSC appears to be less dependent on bcl-2 than adult bone marrow HSC.
Transient Complete Heart Block During Radiofrequency Ablation of a Left Lateral Bypass Tract (1996)

RF catheter ablation of accessory bypass tracts associated with the Wolff-Parkinson-White syndrome has become an accepted and widespread therapy. When bypass tracts are located in the free wall of the left ventricle, a single catheter technique may be utilized. A single catheter is placed via the femoral artery, across the aortic valve into the left ventricle. Mapping is performed during sinus rhythm, and ablation performed at the site of recording of Kent bundle activation. We describe a case of a patient with Wolff-Parkinson-White syndrome presenting with rapid atrial fibrillation requiring cardioversion. This patient subsequently underwent catheter ablation of a left free-wall bypass tract using the single catheter technique. At baseline, preexcitation and right bundle branch block (RBBB) were present on the ECG. During catheter ablation of the accessory pathway, transient complete AV block was seen. This was felt likely to be due to trauma to the His bundle, or more likely to the left bundle branch, as the ablation catheter crossed the aortic valve. The bypass tract was successfully ablated after placement of a temporary right ventricular pacemaker. AV conduction resumed with a pattern of RBBB. A temporary right ventricular pacing catheter should be placed prior to RF ablation of left-sided bypass tracts when the ECG is also suggestive of RBBB.
Spatial gradients in cell wall composition and transcriptional profiles along elongating maize internodes (2014)

The data indicated that the enzymic products of genes involved in cell wall synthesis and modification remain active right along the maturation zone of elongating maize internodes, despite the fact that corresponding transcript levels peak earlier, near or in the transition zone.
Indolent Systemic Mastocytosis with Elevated Serum Tryptase, Absence of Skin Lesions, and Recurrent Severe Anaphylactoid Episodes (2005)

Our report confirms the diagnostic value of tryptase in patients with suspected mastocytosis. In addition, the report suggests that the lack of typical skin lesions does not exclude an indolent form of mastocytosis even if the serum tryptase is clearly elevated. Finally, our case further shows that mastocytosis can be an important differential diagnosis to be considered in patients with unexplained anaphylactoid or other mediator-related symptoms.
ChemInform Abstract: Simple and Condensed β‐Lactams. Part 18. Anomalous Behavior of ( 3RS,4RS)‐((2RS)‐3‐Acetylthiazolidin‐2‐yl)‐1‐(4‐methoxyphenyl)azetidin‐ 2‐ones Towards Cerium(IV) Ammonium Nitrate (CAN). An Unprecedented Oxidative Ring Transformation. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Mechanisms of degeneration in Parkinson’s disease (2005)

Protein aggregation proceeds through a twostep process that starts with nucleation and proceeds to fibrillization (Figure 1.1). The process of protein aggregation can be understood by considering the process of crystallization. Crystallization exhibits a strong lag phase during which nucleation occurs. Nucleation is the rate-limiting step in crystallization. Once nucleation occurs and crystal niduses are generated, crystal formation occurs rapidly. Protein aggregation exhibits similar phenomena. Protein aggregation begins slowly and exhibits a strong lag phase. During the lag phase, small protofibrils form. Once sufficient numbers of protofibrils have formed, the fibrilsbegin to coalesce to form large fibrils, and the rate of protein aggregation increases greatly (Figure 1.1).
Oncogene KRAS activates fatty acid synthase, resulting in specific ERK and lipid signatures associated with lung adenocarcinoma (2017)

KRAS gene mutation causes lung adenocarcinoma. KRAS activation has been associated with altered glucose and glutamine metabolism. Here, we show that KRAS activates lipogenesis, and this activation results in distinct proteomic and lipid signatures. By gene expression analysis, KRAS is shown to be associated with a lipogenesis gene signature and specific induction of fatty acid synthase (FASN). Through desorption electrospray ionization MS imaging (DESI-MSI), specific changes in lipogenesis and specific lipids are identified. By the nanoimmunoassay (NIA), KRAS is found to activate the protein ERK2, whereas ERK1 activation is found in non-KRAS-associated human lung tumors. The inhibition of FASN by cerulenin, a small molecule antibiotic, blocked cellular proliferation of KRAS-associated lung cancer cells. Hence, KRAS is associated with activation of ERK2, induction of FASN, and promotion of lipogenesis. FASN may be a unique target for KRAS-associated lung adenocarcinoma remediation.
Poststatin, a New Inhibitor of Prolyl Endopeptidase. VIII. Endopeptidase Inhibitory Activity of Non-peptidyl Poststatin Analogues. (1996)

Non-peptidyl postatin analogues, (S)-N-substituted-2-[2-(1-acylpyrrolidinyl)]-2-oxoacetamides were synthesized and examined for their inhibitory activity against prolyl endopeptidase and cathepsin B in vitro. Many compounds showed stronger activity than natural poststatin, a pentapeptide. Among them, (S)-N-cyclohexyl-2-oxo-2-[2-(1-(3-phenoxybenzoyl)pyrrolidinyl)]ace tamide (22) and (S)-N-cyclohexyl-2-[2-(1-(2-naphthoyl)pyrrolidinyl)]-2-oxoacetamide++ + (19) indicated IC50 value of 5.8 and 8.2 ng/ml for prolyl endopeptidase inhibition respectively. None of these compounds possess significant inhibitory activities against cathepsin B, a cysteine protease. These results indicate that these compounds are more selective inhibitors against prolyl endopeptidase than is natural poststatin.
Proliferation of adult human bronchial epithelial cells without a telomere maintenance mechanism for over 200 population doublings (2019)

To date, there is no direct evidence of telomerase activity in adult lung epithelial cells, but typical culture conditions only support cell proliferation for 30-40 population doublings (PD), a point at which telomeres remain relatively long. Here we report that in in vitro low stress culture conditions consisting of a fibroblast feeder layer, rho-associated coiled coil protein kinase inhibitor (ROCKi), and low oxygen (2%), normal human bronchial epithelial basal progenitor cells (HBECs) divide for over 200 PD without engaging a telomere maintenance mechanism (almost four times the "Hayflick limit"). HBECs exhibit critically short telomeres at 200 PD and the population of cells start to undergo replicative senescence. Subcloning these late passage cells to clonal density, to mimic lung injury in vivo, selects for rare subsets of HBECs that activate low levels of telomerase activity to maintain short telomeres. CRISPR/Cas9 knockout of human telomerase reverse transcriptase or treatment with the telomerase-mediated telomere targeting agent 6-thio-2'deoxyguanosine abrogates colony growth in these late passage cultures (>200 PD) but not in early passage cultures (<200 PD). To our knowledge, this is the first study to report such long-term growth of HBECs without a telomere maintenance mechanism. This report also provides direct evidence of telomerase activation in HBECs near senescence when telomeres are critically short. This novel cell culture system provides an experimental model to understand how telomerase is regulated in normal adult tissues.
Numerical Study of Large Footprint (24 × 24 mm2) Silicon-Based Embedded Microchannel Three-Dimensional Manifold Coolers (2022)

Abstract Silicon-based embedded microchannel with three-dimensional (3D) manifold (MF) μ-cooler offers lower pressure drop and increased heat removal capability (&amp;gt;1 kW/cm2) for microprocessors and power electronics cooling using single-phase water. In this paper, we present a thermal–fluidic numerical analysis of silicon-embedded microchannel cooling. We develop a full-scale computational fluid dynamics (CFD) model of a large footprint (24 × 24 mm2) device having embedded microchannels and a 3D manifold. It is found that the pressure/velocity distributions at three different critical regions inside the inlet manifold have a significant impact on the temperature distribution. A previous study reported a shift of the chip temperature hot-spot at high flow rates; this study delves deep into the flow and pressure variations within the MF and cold plate (CP) that leads to this shift. This study also investigates the degree of flow maldistribution, first between the manifold channels caused by the plenum and then between the cold plate channels caused by individual MF channels. Finally, this study concludes with a comparison between two different 3D manifold inlet channel heights. The comparison reveals that the manifold with 1.5 mm thickness can reduce the pressure drop by a factor of 4 while maintaining the same thermal resistance of 0.04 K cm2/W, thus indicating an increase in the coefficient of performance (COP) by a factor of 4, compared with a manifold thickness of 0.7 mm.
Route to the Synthesis of Binder-Free SWCNT Solids with Enhanced Mechanical Properties (2006)

Binder‐free macroscopic single‐walled carbon nanotube (SWCNT) solids were prepared by the hot‐pressing and the spark plasma sintering (SPS) of purified SWCNTs at temperatures of 1000, 1400 and 1800°C under a pressure of 120 MPa. The effects of processing conditions of the SWCNT solids on mechanical properties and microstructures were investigated. The SPS method was useful to increase the Young’s modulus and fracture strength of the SWCNT solid with respect to the hot‐pressing method. The mechanical properties of the SWCNT solids prepared by SPS were always higher than those of the SWCNT solids prepared by hot‐pressing under the identical processing temperature. The maximum value for the average Young’s modulus and fracture strength were 25.1 GPa and 106.8 MPa, respectively. TEM observation revealed that the high temperature treatment has converted some part of the SWCNTs into graphite‐like materials and the rest of the SWCNTs remained buried into the above structure. The mechanical properties of the SWCNT solids were increased with the increasing processing temperature, reflecting probably the improvement of interfacial strength between SWCNTs and graphite‐like materials.
Rewriting bulk photoalignment of nematic liquid crystals in a two-step exposure system (2021)

This presentation reveals the re-writability property of azobenzene liquid crystal photoalignment. Stable in thermal fluctuations, one can change existing photoalignment by exposing it to polarized light in the visible regime. One can use this unique property by patterning photoalignment through the liquid crystal bulk in that the sample’s front and back have differing director orientations. Photoalignment using linear polarized light as well as complex polarizations will be covered. No surface alignment on sample substrates is necessary because the azobenzene is mixed with the liquid crystal in-situ in sample preparation.
Symptomatic atherosclerosis is associated with an altered gut metagenome (2012)

Recent findings have implicated the gut microbiota as a contributor of metabolic diseases through the modulation of host metabolism and inflammation. Atherosclerosis is associated with lipid accumulation and inflammation in the arterial wall, and bacteria have been suggested as a causative agent of this disease. Here we use shotgun sequencing of the gut metagenome to demonstrate that the genus Collinsella was enriched in patients with symptomatic atherosclerosis, defined as stenotic atherosclerotic plaques in the carotid artery leading to cerebrovascular events, whereas Roseburia and Eubacterium were enriched in healthy controls. Further characterization of the functional capacity of the metagenomes revealed that patient gut metagenomes were enriched in genes encoding peptidoglycan synthesis and depleted in phytoene dehydrogenase; patients also had reduced serum levels of β-carotene. Our findings suggest that the gut metagenome is associated with the inflammatory status of the host and patients with symptomatic atherosclerosis harbor characteristic changes in the gut metagenome. The gut microbiota has emerged as an environmental factor that can influence the development of obesity and diabetes. Here, Karlsson et al. report compositional and functional alterations of the gut metagenome in patients with symptomatic atherosclerosis.
Sensitive Amino Acid Composition and Chirality Analysis with the Mars Organic Analyzer (MOA) (2004)

Detection of life on Mars requires definition of a suitable biomarker and development of sensitive yet compact instrumentation capable of performing in situ analyses. Our studies are focused on amino acid analysis because amino acids are more resistant to decomposition than other biomolecules, and because amino acid chirality is a well-defined biomarker. Amino acid composition and chirality analysis has been previously demonstrated in the lab using microfabricated capillary electrophoresis (CE) chips. To analyze amino acids in the field, we have developed the Mars Organic Analyzer (MOA), a portable analysis system that consists of a compact instrument and a novel multi-layer CE microchip.
Postharvest treatments and maturity stages impact sensory attributes and shelf life of tomato fruits var. Pearson kept in Zero Energy Cool Chamber (2022)

The investigation has been carried out under ZECC conditions located at the research farm of agriculture faculty of Kabul University, Afghanistan. The objective was to understand the effect of postharvest treatments and harvesting stages on the shelf life and sensory quality of tomato fruits. It was found that both main factors had a significant effect and the highest shelf life noted for the fruits of H1(turning color stage) and D1 (dipped in 6 % CaCl2 solution) was 26.19 and 25.17 days, respectively. At the end of the storage period, the final evaluation average scores for overall sensory attributes of turning color fruits were higher whereas it was noted lower for light red color fruits compared with initial scores. The highest scores for all attributes such as color, flesh texture, flavor, and overall acceptance were noted for the fruits of H1 and D1 respectively. Thus, the turning color stage has seen as a suitable harvesting stage and then followed by pink color stage of the tomatoes of the Pearson variety that could be considered for various purposes after storage respectively. The 6 % CaCl2 solution could increase tomatoes shelf life and maintain the quality that it had retained the fruits sensory attributes to an acceptable level
The lin-11 LIM domain transcription factor is necessary for morphogenesis of C. elegans uterine cells (1999)

The Caenorhabditis elegans hermaphrodite egg-laying system comprises several tissues, including the uterus and vulva. lin-11 encodes a LIM domain transcription factor needed for certain vulval precursor cells to divide asymmetrically. Based on lin-11 expression studies and the lin-11 mutant phenotype, we find that lin-11 is also required for C. elegans uterine morphogenesis. Specifically, lin-11 is expressed in the ventral uterine intermediate precursor (pi) cells and their progeny (the utse and uv1 cells), which connect the uterus to the vulva. Like (pi) cell induction, the uterine lin-11 expression responds to the uterine anchor cell and the lin-12-encoded receptor. In wild type animals, the utse, which forms the planar process at the uterine-vulval interface, fuses with the anchor cell. We found that, in lin-11 mutants, utse differentiation was abnormal, the utse failed to fuse with the anchor cell and a functional uterine-vulval connection was not made. These findings indicate that lin-11 is essential for uterine-vulval morphogenesis.
SAC: Semantic Attention Composition for Text-Conditioned Image Retrieval (2022)

The ability to efficiently search for images is essential for improving the user experiences across various products. Incorporating user feedback, via multi-modal inputs, to navigate visual search can help tailor retrieved results to specific user queries. We focus on the task of text-conditioned image retrieval that utilizes support text feedback alongside a reference image to retrieve images that concurrently satisfy constraints imposed by both inputs. The task is challenging since it requires learning composite image-text features by incorporating multiple cross-granular semantic edits from text feedback and then applying the same to visual features. To address this, we propose a novel framework SAC which resolves the above in two major steps: "where to see" (Semantic Feature Attention) and "how to change" (Semantic Feature Modification). We systematically show how our architecture streamlines the generation of text-aware image features by removing the need for various modules required by other state-of-art techniques. We present extensive quantitative, qualitative analysis, and ablation studies, to show that our architecture SAC outperforms existing techniques by achieving state-of-the-art performance on 3 benchmark datasets: FashionIQ, Shoes, and Birds-to-Words, while supporting natural language feedback of varying lengths.
Learning appearance and transparency manifolds of occluded objects in layers (2003)

By mapping a set of input images to points in a low-dimensional manifold or subspace, it is possible to efficiently account for a small number of degrees of freedom. For example, images of a person walking can be mapped to a one-dimensional manifold that measures the phase of the person's gait. However, when the object is moving around the frame and being occluded by other objects, standard manifold modeling techniques (e.g., principal components analysis, factor analysis, locally linear embedding) try to account for global motion and occlusion. We show how factor analysis can be incorporated into a generative model of layered, 2.5-dimensional vision, to jointly locate objects, resolve occlusion ambiguities, and learn models of the appearance manifolds of objects. We demonstrate the algorithm on a video consisting of four occluding objects, two of which are people who are walking, and occlude each other for most of the duration of the video. Whereas standard manifold modeling techniques fail to extract information about the gaits, the layered model successfully extracts a periodic representation of the gait of each person.
Nanoscale Kirkendall Effect and Oxidation Kinetics in Copper Nanocrystals Characterized by Real‐Time, In Situ Optical Spectroscopy (2014)

The low‐temperature oxidation of ≈10 nm diameter copper nanocrystals is characterized using in situ UV–vis absorbance spectroscopy and observed to lead to hollow copper oxide shells. The kinetics of the oxidation of solid Cu nanocrystals to hollow Cu 2 O nanoparticles is monitored in real‐time via the localized surface plasmon resonance response of the copper. A reaction‐diffusion model for the formation of hollow nanoparticles is fit to the measured time for complete Cu nanocrystal oxidation, and is used to quantify the diffusion coefficient of Cu in Cu 2 O and the activation energy of the oxidation process. The diffusivity measured here in single‐crystalline nanoscale systems is 1–5 orders of magnitude greater than in comparable systems in the bulk, and have an Arrhenius dependence on temperature with an activation energy for diffusion of 37.5 kJ mol −1 for 85 °C ≤ T ≤ 205 °C. These diffusion parameters are measured in some of the smallest metal systems and at the lowest oxidation temperatures yet reported, and are enabled by the unique nanoscale single‐crystalline material and the in situ characterization technique.
INFRARED SPECTRA OF THE REACTION BETWEEN METAL ATOMS AND WATER MOLECULES IN AN ARGON MATRIX (1979)

Author Institution:
HeLa Cell Entry by Guanidinium‐Rich β‐Peptides: Importance of Specific Cation–Cell Surface Interactions (2007)

Short cationic oligomers, including arginine-rich peptides and analogous beta-amino acid oligomers ("beta-peptides"), can enter the cytoplasm and nucleus of a living cell from the extracellular medium. It seems increasingly clear that multiple entry pathways are possible, depending upon the structure of the guanidinium-rich molecule, the type of cell, and other factors. We have previously shown that conformational stability and spatial clustering of guanidinium groups increase the HeLa cell entry efficiency of short helical beta-peptides bearing six guanidinium groups, results that suggest that these beta-peptides could be useful tools for studying the entry process. Here we describe studies intended to identify the point in the entry process at which helix stability and spatial arrangement of guanidinium groups exert their effect. Our results suggest that key distinctions involve the mode of interaction between different guanidinium-rich beta-peptides and the HeLa cell surface. A specific guanidinium display appears to be required for proper engagement of cell-surface heparan sulfate proteoglycans and concomitant induction of endocytic uptake.
<b><i>Porphyromonas gingivalis </i></b>Gingipains Selectively Reduce CD14 Expression, Leading to Macrophage Hyporesponsiveness to Bacterial Infection (2014)

Cysteine proteases (gingipains) from Porphyromonas gingivalis are key virulence factors in chronic periodontitis. Innate immune receptors CD14, Toll-like receptor (TLR) 2 and TLR4 are important in P. gingivalis recognition. We examined the ability of gingipains to cleave CD14, TLR2 and TLR4, and the consequences for the cellular response to bacterial challenge. Macrophages were exposed to Arg (RgpA and RgpB)- and Lys (Kgp)-gingipains, and residual expression of TLR2, TLR4 and CD14 was determined by flow cytometry. The cellular response to live bacteria following exposure to purified gingipains was evaluated by TNFα production and bacterial phagocytosis. RgpA and Kgp decreased CD14 detection in a concentration (p = 0.0000002)- and time (p = 0.03)-dependent manner, whereas RgpB had no significant effect. TLR2 and TLR4 expression were unaffected. Reduction in CD14 expression was more efficient with Lys-gingipain than with Arg-gingipain. A reduced CD14 surface level correlated with decreased TNFα secretion and bacterial phagocytosis following challenge with live P. gingivalis, but the response to heat-killed bacteria was unaffected. Therefore, gingipains reduce CD14 expression without affecting expression of the bacterial-sensing TLRs. Reduced CD14 expression depends on the gingipain hemagglutinin/adhesion site and results in macrophage hyporesponsiveness to bacterial challenge. Further studies are needed to determine if reduced CD14 expression is linked to periodontitis induced by P. gingivalis.