gebhart/patrepeval huggingface dataset:
Mouse embryonic stem cells can differentiate via multiple paths to the same state (2017)

Abstract In embryonic development, cells must differentiate through stereotypical sequences of intermediate states to generate mature states of a particular fate. By contrast, direct programming can generate similar fates through alternative routes, by directly expressing terminal transcription factors. Yet the cell state transitions defining these new routes are unclear. We applied single-cell RNA sequencing to compare two mouse motor neuron differentiation protocols: a standard protocol approximating the embryonic lineage, and a direct programming method. Both undergo similar early neural commitment. Then, rather than transitioning through spinal intermediates like the standard protocol, the direct programming path diverges into a novel transitional state. This state has specific and abnormal gene expression. It opens a ‘loop’ or ‘worm hole’ in gene expression that converges separately onto the final motor neuron state of the standard path. Despite their different developmental histories, motor neurons from both protocols structurally, functionally, and transcriptionally resemble motor neurons from embryos.
1.4.3 Concepts for accurate electrical conductivity measurement of liquids in industrial process analytics (2019)

The electrical conductivity of liquids is of interest in many industrial processes, for example in water desalination, cleaning, mixing of different liquids, analysis of acids and bases, etc. In this contribution, specifically two-electrode conductivity sensors are discussed. A problem with this type of sensor is that a double layer (DL) is given at the interfaces between each of the electrodes and the liquid, resulting in varying and unpredictable diffusion capacitances. For this reason, the electrical resistance of the liquid is not directly accessible from measurements of the sensor input impedance at low frequencies. For accurate determination of the conductivity, the parasitic and disturbing diffusion capacitances, as well as the unknown capacitance of the liquid and the parasitic sensor capacitance have to be eliminated from the measured impedance. The approach in electrical impedance spectroscopy (EIS) is to measure over a very large frequency range for explicitly determining and eliminating the unknown network elements. The motivation behind the work presented here is to allow for precise conductivity measurement at only low frequencies in the range of some kHz. Very advantageously with this, low-cost and low-demanding sensor electronics can be utilized for the realization of according industrial sensors. An equivalent circuit network model of the sensor has been analyzed in detail for this purpose. Approaches for estimating the resistance of the liquid from low frequency measurements of the sensor input impedance are presented and discussed. Finally, the resulting systematic measurement error has been evaluated based on the network model and experimentally.
Intrinsic Fano Interference of Localized Plasmons in Pd Nanoparticles (2009)

Palladium (Pd) nanoparticles exhibit broad optical resonances that have been assigned to so-called localized surface plasmons (LSPs). The resonance's energy varies with particle shape in a similar fashion as is well known for LSPs in gold and silver nanoparticles, but the line-shape is always anomalously asymmetric. We here show that this effect is due to an intrinsic Fano interference caused by the coupling between the plasmon response and a structureless background originating from interband transitions. The conclusions are supported by experimental and numerical simulation data of Pd particles of different shape and phenomenologically analyzed in terms of the point dipole polarizability of spheroids. The latter analysis indicates that the degree of Fano asymmetry is simply linearly proportional to the imaginary part of the interband contribution to the metal dielectric function.
Supplementary Figure 4 from Personalized Chemotherapy Profiling Using Cancer Cell Lines from Selectable Mice (2023)

&lt;p&gt;PDF file - 1505K, Selection of pancreatic cancer cell line, Panc502.&lt;/p&gt;
Supplementary Figure 2 from IGKV3 Proteins as Candidate “Off-the-Shelf” Vaccines for Kappa-Light Chain–Restricted B-Cell Non-Hodgkin Lymphomas (2023)

&lt;p&gt;PDF file, 331KB, Cross-reactive CTL responses elicited by native IGKV3-20 epitopes.&lt;/p&gt;
Half‐Life Extension with Pharmaceutical Formulations: Nanoparticles by the Miniemulsion Process (2012)

This chapter contains sections titled: Introduction Polymeric Nanoparticles Particles Obtained by Radical Polymerization and Their Functionalization Other Polyreactions in Miniemulsion Formation of Nanocapsules and Their Functionalization Encapsulation of Markers and Detection of Nanoparticles in Biological Systems Release of Materials Conclusion Acknowledgment References
Nonclassical Activation of Carbon Monoxide by Organoactinides (1980)

This article reviews recent results on the carbonylation chemistry of bis(pentamethylcyclopentadienyl) thorium and uranium hydrocarbyl and dialkylamide complexes. Facile migratory insertion of carbon monoxide into metal-carbon and metal-nitrogen bonds is observed. In several cases bihapfcoacyl and bihaptocarbamoyl complexes were isolated and characterized by single crystal X-ray diffraction. The great strength of the metal-oxygen bonding in these species is evident in metrical and spectral data, as well as in the reaction chemistry, which is decidedly alkoxycarbenelike. In the case of the bis(pentamethylcyclopentadienyl) actinide dialkyls, the final carbonylation products are C-C coupled cis-1,2-enediolate complexes, while for the corresponding bis(dialkylamides), the products are bis(carbamoyl) species. Both types of compound have been characterized by X-ray diffraction. The carbon monoxide chemistry observed here may be of relevance to mechanistic discussions of catalytic CO reduction, especially that involving actinide oxide or actinide oxide supported catalysts.
Enabling High Efficiency Direct Injection Engine with Naphtha Fuel through Partially Premixed Charge Compression Ignition Combustion (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;More stringent emissions standards along with higher fuel economy demands have obliged auto makers to develop technical solutions that exploit synergistic features from gasoline and diesel engines. To minimize NOx and soot trade-off, diesel powertrain has been developed to adopt increasingly complex and expensive technology such as extremely high pressure fuel injection systems, low pressure EGR, and variable valve timing. These attempts are associated with promoting Partially Premixed Charge Compression Ignition (PPC-CI) combustion via increasing mixing time and ignition delay. Alternatively, PPC-CI combustion can be achieved easier by using fuels with higher resistance to auto-ignition than conventional diesel fuel. Previous work has demonstrated the possibility of reducing the cost of future diesel after-treatment systems by using gasoline-like fuels. In this study, we start with a 0.5-liter single-cylinder direct injection spark ignition (DISI) engine and demonstrate that fuel economy can be improved significantly by running it in PPC-CI mode. Naphtha, less processed refinery stream in the gasoline boiling and carbon number range, but with lower Octane Number, has been run in a 12:1 compression ratio single-cylinder engine with DISI fuel system and shallow oval-type bowl piston. Both light and heavy Naphtha were successfully run in PPC-CI mode with regular valve events and intake charge boosting at six engine running conditions representative of a typical urban driving cycle including idle. Very low NOx level was achieved through high EGR and advanced injection timings to segregate the fuel injection from heat release. When compared to a Stoichiometric SI operation with optimal valve timings, 19% weighted cycle average fuel consumption reduction was achieved. This result demonstrates that an engine equipped with a low cost DI system could offer noticeably better efficiency through PPC-CI combustion, especially when run with Naphtha, which can provide lower CO₂ emission in a refinery process. Although further work is needed to develop a practical engine, high efficiency, reduced system cost and overall CO₂ footprint benefits can be achieved by matching the fuel and the combustion system.&lt;/div&gt;&lt;/div&gt;
Mid-infrared silicon-on-sapphire waveguide coupled photonic crystal microcavities (2015)

We experimentally demonstrate a photonic crystal (PC) microcavity side coupled to a W1.05 photonic crystal waveguide fabricated in silicon-on-sapphire working in mid-IR regime at 3.43 μm. Using a fixed wavelength laser source, propagation characteristics of PC waveguides without microcavity are characterized as a function of lattice constant to determine the light line position, stop gap, and guided mode transmission behavior. The resonance of an L21 PC microcavity coupled to the W1.05 PCW in the guided mode transmission region is then measured by thermal tuning of the cavity resonance across the source wavelength. Resonance quality factor ∼3500 is measured from the temperature dependency curve.
Acidic Fibroblast Growth Factor Enhances Peripheral Nerve Regeneration in Vivo (1989)

Cordeiro, Peter G. M.D.; Seckel, Brooke R. M.D.; Lipton, Stuart A. M.D., Ph.D.; D'Amore, Patricia A. Ph.D.; Wagner, John Ph.D.; Madison, Roger Ph.D.
Reduction of Carboxylic Acids to Alcohols via Manganese(I) Catalyzed Hydrosilylation (2021)

The reduction of carboxylic acids to the respective alcohols, in mild conditions, was achieved using [MnBr(CO)<sub>5</sub>] as the catalyst and bench stable PhSiH<sub>3</sub> as the reducing agent. It was shown that the reaction with the earth-abundant metal catalyst could be performed either with a catalyst loading as low as 0.5 mol %, rare with the use of [MnBr(CO)<sub>5</sub>], or on a gram scale employing only 1.5 equiv of PhSiH<sub>3</sub>, the lowest amount of silane reported to date for this transformation. Kinetic data and control experiments have provided initial insight into the mechanism of the catalytic process, suggesting that it proceeds via the formation of silyl ester intermediates and ligand dissociation to generate a coordinatively unsaturated Mn(I) complex as the active species.
Interactions between environmental sensitivity and gut microbiota are associated with biomarkers of stress-related psychiatric symptoms (2023)

Abstract Background Humans vary in their sensitivity to stressful and supportive environments and experiences. Such individual differences in environmental sensitivity are associated with mechanisms of stress-related psychiatric symptoms. In recent years, researchers have focused on bidirectional interactions in the brain-gut-microbiota axis as a neurophysiological pathway contributing to the mechanisms of stress-related psychiatric symptoms, and evidence is rapidly accumulating. Methods Data on environmental sensitivity, gut microbiota, gut permeability (lipopolysaccharide-binding protein; LBP) and inflammation (C-reactive protein; CRP) were collected from 90 adults (50% female; M age = 42.1; SD age = 10.0). Environmental sensitivity was measured using a self-report questionnaire. Study participants’ feces were analyzed, and observed operational taxonomic units for richness, Shannon’s index for evenness, and phylogenetic diversity for biodiversity were evaluated as indicators of gut microbiota. In addition, participants’ serum was analyzed for CRP and LBP. We investigated whether the interaction between environmental sensitivity and gut microbiota is associated with biomarkers of inflammation and gut permeability. Results The interaction between environmental sensitivity and gut microbiota (excluding the Shannon’s index) explained the levels of these biomarkers. Individuals with high environmental sensitivity displayed higher levels of CRP and LBP, when the richness and diversity of the gut microbiota was low. However, even highly susceptible individuals had lower levels of CRP and LBP, when the richness and diversity of the gut microbiota was high. Conclusions Our study indicates that high environmental sensitivity can be a risk factor for inflammation and gut permeability, when the gut microbiota diversity is low, suggesting a brain-gut-microbiota axis interaction.
The Normal Counterpart of IgD Myeloma Cells in Germinal Center Displays Extensively Mutated IgVH Gene, Cμ–Cδ Switch, and λ Light Chain Expression (1998)

Human myeloma are incurable hematologic cancers of immunoglobulin-secreting plasma cells in bone marrow. Although malignant plasma cells can be almost eradicated from the patient's bone marrow by chemotherapy, drug-resistant myeloma precursor cells persist in an apparently cryptic compartment. Controversy exists as to whether myeloma precursor cells are hematopoietic stem cells, pre-B cells, germinal center (GC) B cells, circulating memory cells, or plasma blasts. This situation reflects what has been a general problem in cancer research for years: how to compare a tumor with its normal counterpart. Although several studies have demonstrated somatically mutated immunoglobulin variable region genes in multiple myeloma, it is unclear if myeloma cells are derived from GCs or post-GC memory B cells. Immunoglobulin (Ig)D-secreting myeloma have two unique immunoglobulin features, including a biased lambda light chain expression and a Cmu-Cdelta isotype switch. Using surface markers, we have previously isolated a population of surface IgM-IgD+CD38+ GC B cells that carry the most impressive somatic mutation in their IgV genes. Here we show that this population of GC B cells displays the two molecular features of IgD-secreting myeloma cells: a biased lambda light chain expression and a C&mu-Cdelta isotype switch. The demonstration of these peculiar GC B cells to differentiate into IgD-secreting plasma cells but not memory B cells both in vivo and in vitro suggests that IgD-secreting plasma and myeloma cells are derived from GCs.
Learning Fashion Compatibility Across Apparel Categories for Outfit Recommendation (2019)

This paper addresses the problem of generating recommendations for completing the outfit given that a user is interested in a particular apparel item. The proposed method is based on a siamese network used for feature extraction followed by a fully-connected network used for learning a fashion compatibility metric. The embeddings generated by the siamese network are augmented with color histogram features motivated by the important role that color plays in determining fashion compatibility. The training of the network is formulated as a maximum a posteriori (MAP) problem where Laplacian distributions are assumed for the filters of the siamese network to promote sparsity and matrix-variate normal distributions are assumed for the weights of the metric network to efficiently exploit correlations between the input units of each fully-connected layer.
Microretroreflector-Sedimentation Immunoassays for Pathogen Detection (2014)

Point-of-care detection of pathogens is medically valuable but poses challenging trade-offs between instrument complexity and clinical and analytical sensitivity. Here we introduce a diagnostic platform utilizing lithographically fabricated micron-scale forms of cubic retroreflectors, arguably one of the most optically detectable human artifacts, as reporter labels for use in sensitive immunoassays. We demonstrate the applicability of this novel optical label in a simple assay format in which retroreflector cubes are first mixed with the sample. The cubes are then allowed to settle onto an immuno-capture surface, followed by inversion for gravity-driven removal of nonspecifically bound cubes. Cubes bridged to the capture surface by the analyte are detected using inexpensive, low-numerical aperture optics. For model bacterial and viral pathogens, sensitivity in 10% human serum was found to be 10(4) bacterial cells/mL and 10(4) virus particles/mL, consistent with clinical utility.
Infrared Laser Nerve Stimulation as a Potential Diagnostic Method for Intra-Operative Identification and Preservation of the Prostate Cavernous Nerves (2014)

The cavernous nerves, which course along the surface of the prostate gland, are responsible for erectile function. Urologic surgeons are challenged in preserving these nerves during prostate cancer surgery, due to their microscopic nature and variable location among patients. Current intra-operative diagnostic methods for identifying, imaging, and preserving these delicate nerves during removal of a cancerous prostate gland remain sub-optimal. Our laboratory is focused on developing optical-based methods for detecting these nerves. This manuscript reviews progress in pre-clinical development of infrared optical nerve stimulation as a potential technique for identifying the cavernous nerves. Critical laser parameters for safe and reliable stimulation of the cavernous nerves, development of laser and fiber optic probe instrumentation, and novel approaches are presented.
Calibration and 3D measurement from Martian terrain images (2002)

An on-Mars calibration procedure of a planetary lander vision system is presented. It is based on developments in computer vision. The calibration is retrieved from the images of the Mars terrain. The procedure is based on the relations between multiple views of the same scene. It allows us to retrieve the calibration on Mars without any additional requirements on the system. Once the system has been calibrated, the same images can be used to estimate a digital elevation map (DEM) of the environment around the lander. The images are first processed pairwise using a stereo algorithm yielding sub-pixel disparity maps. An algorithm was developed to efficiently extract a DEM from the disparity maps. The DEM can be generated at any desired resolution (interpolating if necessary) and occlusions are easily taken into account.
MenDEL: automated search of BAC sets covering long DNA regions of interest (2022)

Abstract Motivation Synthetic genomics as a field seeks to synthesize large regions of genomes from the ground up. Such large-scale projects, especially in complex genomes can rely on pre-existing BAC (Bacterial Artificial Chromosome) libraries as starting material to reduce cost. However, choosing BACs that cover long DNA regions, especially those that require many BACs, is a manual, idiosyncratic, time consuming, and error prone process. Automating this work would make the assembly of large DNA constructs more efficient. Results We have developed MenDEL – a web-based DNA design application, that provides efficient tools for finding BACs that cover long regions of interest and allow for sorting results based on multiple user defined criteria - total length, number of BACs, longest BAC. etc. In addition, it enables the user to find a combination of BACs from pre-existing libraries that cover a region of interest not found in any single BAC. Availability and Implementation MenDEL application is available to registered users at https://mendel-isg.nyumc.org , Java code used in the application to find BAC sets is available at https://github.com/MendelProject/BACFinder
Efficacy of compartmental administration of immunotoxin LMB-1 (B3-LysPE38) in a rat model of carcinomatous meningitis. (1995)

LMB-1 (B3-LysPE38) is an immunotoxin composed of the tumor-reactive monoclonal antibody B3 and a genetically engineered form of Pseudomonas exotoxin. Monoclonal antibody B3 reacts with a carbohydrate epitope that is found on a number of solid tumors (e.g., breast, ovarian, and lung carcinomas) that frequently invade the intrathecal space, causing neoplastic meningitis. The Pseudomonas exotoxin has been engineered to remove the binding domain to eliminate nonspecific binding. A model of human neoplastic meningitis using rats bearing the human epidermoid carcinoma A431 was used for therapeutic studies of immunotoxin LMB-1. Therapy was initiated 3 days after injection of the tumor cells, which was one third of the median survival time of untreated rats. A single intrathecal injection of 40 microgram increased median survival from 9 days with saline injection to 16 days (78%, P < 0.001), and a single dose of 200 microgram increased median survival to 25 days (188%, P < 0. 001). Three doses of 40 or 200 microgram given on days 3, 6, and 8 significantly increased the median survival of 9.5 days associated with saline injection to 40.5 days (326% increase) and 33.0 days (247% increase), respectively, with two long-term survivors (191-day survival) in each treatment group. LMB-1 had no therapeutic effect on the treatment of two B3 antigen-negative neoplastic meningitis models. Treatment of the antigen-positive A431 neoplastic meningitis with B3 alone or a nonspecific monoclonal, MOPC, coupled to the engineered Pseudomonas exotoxin produced no survival effects. Nontumor-bearing athymic rats showed no toxicity with a single dose of either 40 microgram or 200 microgram, or 3 doses of 40 microgram. However, when they were given three doses of 200 microgram, these rats showed weight loss and loss of neurological function, and two of eight animals died. These studies indicate that, in the range of the most therapeutically effective dosage, the immunotoxin LMB-1 is tolerated in the intrathecal space and should be considered for human intrathecal trials.
CXCL12 Induces Connective Tissue Growth Factor Expression in Human Lung Fibroblasts through the Rac1/ERK, JNK, and AP-1 Pathways (2014)

CXCL12 (stromal cell-derived factor-1, SDF-1) is a potent chemokine for homing of CXCR4+ fibrocytes to injury sites of lung tissue, which contributes to pulmonary fibrosis. Overexpression of connective tissue growth factor (CTGF) plays a critical role in pulmonary fibrosis. In this study, we investigated the roles of Rac1, extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and activator protein-1 (AP-1) in CXCL12-induced CTGF expression in human lung fibroblasts. CXCL12 caused concentration- and time-dependent increases in CTGF expression and CTGF-luciferase activity. CXCL12-induced CTGF expression was inhibited by a CXCR4 antagonist (AMD3100), small interfering RNA of CXCR4 (CXCR4 siRNA), a dominant negative mutant of Rac1 (RacN17), a mitogen-activated protein kinase (MAPK) kinase (MEK) inhibitor (PD98059), a JNK inhibitor (SP600125), a p21-activated kinase inhibitor (PAK18), c-Jun siRNA, and an AP-1 inhibitor (curcumin). Treatment of cells with CXCL12 caused activations of Rac1, Rho, ERK, and c-Jun. The CXCL12-induced increase in ERK phosphorylation was inhibited by RacN17. Treatment of cells with PD98059 and SP600125 both inhibited CXCL12-induced c-Jun phosphorylation. CXCL12 caused the recruitment of c-Jun and c-Fos binding to the CTGF promoter. Furthermore, CXCL12 induced an increase in α-smooth muscle actin (α-SMA) expression, a myofibroblastic phenotype, and actin stress fiber formation. CXCL12-induced actin stress fiber formation and α-SMA expression were respectively inhibited by AMD3100 and CTGF siRNA. Taken together, our results suggest that CXCL12, acting through CXCR4, activates the Rac/ERK and JNK signaling pathways, which in turn initiates c-Jun phosphorylation, and recruits c-Jun and c-Fos to the CTGF promoter and ultimately induces CTGF expression in human lung fibroblasts. Moreover, overexpression of CTGF mediates CXCL12-induced α-SMA expression.