gebhart/patrepeval huggingface dataset:
Urban-scale Spatial-temporal Variability of Black Carbon and Winter Residential Wood Combustion Particles (2011)

It has been suggested that certain organic aerosol components of wood smoke have enhanced ultraviolet absorption at 370 nm relative to 880 nm in two-wavelength aethalometer black carbon (BC) measurements. This enhanced absorption could serve as an indicator of wood combustion particles (“Delta-C” = UVBC370nm – BC880nm). From August 2009 to October 2010, week-long mobile monitoring campaigns were conducted during each season in Rochester, New York. The temporal and spatial variations of BC and Delta-C were investigated at twelve monitoring sites. A portable two-wavelength aethalometer housed in Clarkson’s Mobile Air Pollution Lab was used for data collection. The average BC concentrations were 0.94 µg/m3, 0.68 µg/m3, 0.47 µg/m3, and 0.81 µg/m3 in summer, winter, spring, and fall, respectively. BC and Delta-C hotspots were identified. Coefficients of divergence (COD) and correlation coefficients (r) were calculated between site pairs to assess the spatial and temporal heterogeneity. High spatial divergence but uniform temporal variation in BC were found for these sites. Winter residential wood combustion (RWC) particles exhibited high spatial heterogeneity as well. In epidemiological studies, BC particles data from a central monitoring site are generally used as the basis in population exposure estimation. These results suggest that one central monitoring site may not adequately represent the actual BC and RWC particle exposure over a whole urban area.
Detection of Protein Analytes via Nanoparticle-Based Bio Bar Code Technology (2006)

We describe a new format for the recently introduced bio bar code technology, which improves the dose response over 10,000-fold and thereby makes this technique analytically useful. Unlike other ultrasensitive protein detection methods, such as immuno-PCR or immuno-RCA, the bio bar code technique does not employ any enzymes to achieve detection limits in the attomolar range. By sandwiching a target between a magnetic bead and an amplifier nanoparticle, a multiplicity of bar code oligonucleotides are released for each captured target analyte. These surrogate bar code targets are then hybridized to microarrays and detected with silver-amplified gold nanoparticle probes. Using PSA detection as a model, we demonstrate a linear dose response over at least 4 orders of magnitude in both target concentration and concomitant signal and a 1000-fold improvement in detection limit compared to the best ELISA system.
Angle-resolved Optical Coherence Tomography with sequential angular selectivity for speckle reduction (2007)

We present a novel method for rapidly acquiring optical coherence tomography (OCT) images at multiple backscattering angles. By angularly compounding these images, high levels of speckle reduction were achieved. Signal-to-noise ratio (SNR) improvements of 3.4 dB were obtained from a homogeneous tissue phantom, which was in good agreement with the predictions of a statistical model of speckle that incorporated the optical parameters of the imaging system. In addition, the fast acquisition rate of the system (10 kHz A-line repetition rate) allowed angular compounding to be performed in vivo without significant motion artifacts. Speckle-reduced OCT images of human dermis show greatly improved delineation of tissue microstructure.
In vivo confirmation of hydration based contrast mechanisms for terahertz medical imaging using MRI (2014)

Terahertz (THz) detection has been proposed and applied to a variety of medical imaging applications in view of its unrivaled hydration profiling capabilities. Variations in tissue dielectric function have been demonstrated at THz frequencies to generate high contrast imagery of tissue, however, the source of image contrast remains to be verified using a modality with a comparable sensing scheme. To investigate the primary contrast mechanism, a pilot comparison study was performed in a burn wound rat model, widely known to create detectable gradients in tissue hydration through both injured and surrounding tissue. Parallel T2 weighted multi slice multi echo (T2w MSME) 7T Magnetic Resonance (MR) scans and THz surface reflectance maps were acquired of a full thickness skin burn in a rat model over a 5 hour time period. A comparison of uninjured and injured regions in the full thickness burn demonstrates a 3-fold increase in average T2 relaxation times and a 15% increase in average THz reflectivity, respectively. These results support the sensitivity and specificity of MRI for measuring in vivo burn tissue water content and the use of this modality to verify and understand the hydration sensing capabilities of THz imaging for acute assessments of the onset and evolution of diseases that affect the skin. A starting point for more sophisticated in vivo studies, this preliminary analysis may be used in the future to explore how and to what extent the release of unbound water affects imaging contrast in THz burn sensing.
A Depth Dependent Quality Metric for Evaluation of Coded Integral Imaging Based 3D-Images (2007)

The two-dimensional quality metric peak-signal-to-noise-ratio (PSNR) is often used to evaluate the quality of coding schemes for integral imaging (II) based 3D-images. The PSNR may be applied to the full II resulting in single accumulate quality metric covering all possible views. Alternatively, it may be applied to each view results in a metric depending on viewing angle. However, both of these approaches fail to capture a coding scheme's distribution of artifacts at different depths within the 3D-image. In this paper we propose a metric that determines the 3D-image quality at different depths. First we introduce this ID measure, and the operations that it is based on, followed by the experimental setup used to evaluate it. Finally, the metric is evaluated on a set of 3D-images; each coded using four different coding schemes and compared with visual inspection of the introduced coding distortion. The results indicate a good correlation with the coding artifacts and their distribution over different depths.
Rare Complement Factor H Variant Associated With Age-Related Macular Degeneration in the Amish (2014)

Data from the cumulative genetic risk score analysis suggests that the variants reported by the AMDGene consortium account for a smaller genetic burden of disease in the Amish compared with the non-Amish Caucasian population. Using exome sequencing data, we identified a novel missense mutation that is shared among a densely affected nuclear Amish family and located in a gene that has been previously implicated in AMD risk.
A novel candidate metastasis-associated gene, mta1, differentially expressed in highly metastatic mammary adenocarcinoma cell lines. cDNA cloning, expression, and protein analyses. (1994)

To understand the genes involved in breast cancer invasion and metastasis, we analyzed a novel candidate metastasis-associated gene, mta1, which was isolated by differential cDNA library screening using the 13762NF rat mammary adenocarcinoma metastatic system. Northern blot analyses showed that the mRNA expression level of the mta1 gene was 4-fold higher in the highly metastatic cell line MTLn3 than in the nonmetastatic cell line MTC.4. The mta1 gene was expressed in various normal rat organs, especially in the testis, suggesting its essential normal function. The mRNA expression levels of the human homologue of this gene also correlated with the metastatic potential in two human breast cancer metastatic systems. The full-length mta1 cDNA sequence contained an open reading frame encoding a protein of 703 amino acid residues, and sequence analysis by data base homology search indicated that mta1 is a novel gene. The Mta1 protein contained several possible phosphorylation sites, and a proline-rich amino acid stretch at the carboxyl-terminal end completely matched the consensus sequence for the src homology 3 domain-binding motif. Using antibodies raised against glutathione S-transferase-Mta1 fusion protein or a synthetic oligopeptide, Western blots showed that the molecular mass of the Mta1 protein was approximately 80 kDa, and the levels of the Mta1 protein also correlated with the metastatic potential, results similar to those obtained from the Northern analyses. Thus, the novel gene mta1 may encode a molecule that is functional in normal cells as well as in breast cancer invasion and metastasis.
Escherichia coli Harboring mcr-1 and bla CTX-M on a Novel IncF Plasmid: First Report of mcr-1 in the United States (2016)

The recent discovery of a plasmid-borne colistin resistance gene, mcr-1 , in China heralds the emergence of truly pan-drug-resistant bacteria ([1][1]). The gene has been found primarily in Escherichia coli but has also been identified in other members of the Enterobacteriaceae in human, animal, food
Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome (2005)

We describe a DNA sequencing technology in which a commonly available, inexpensive epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing automation. We apply this technology to resequence an evolved strain of Escherichia coli at less than one error per million consensus bases. A cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized in a polyacrylamide gel and subjected to automated cycles of sequencing by ligation and four-color imaging. Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents.
Secreted Immunomodulatory Viral Proteins as Novel Biotherapeutics (2004)

Abstract Many viruses have learned to evade or subvert the host antiviral immune responses by encoding and expressing immunomodulatory proteins that protect the virus from attack by elements of the innate and acquired immune systems. Some of these viral anti-immune regulators are expressed as secreted proteins that engage specific host immune targets in the extracellular environment, where they exhibit potent anti-immune properties. We review here viral immunomodulatory proteins that have been tested as anti-inflammatory reagents in animal models of disease caused by excessive inflammation or hyperactivated immune pathways. The potential for such viral molecules for the development of novel drugs to treat immune-based or inflammatory disorders is discussed.
Estimating Protein−Ligand Binding Affinity Using High-Throughput Screening by NMR (2008)

Many of today's drug discovery programs use high-throughput screening methods that rely on quick evaluations of protein activity to rank potential chemical leads. By monitoring biologically relevant protein-ligand interactions, NMR can provide a means to validate these discovery leads and to optimize the drug discovery process. NMR-based screens typically use a change in chemical shift or line width to detect a protein-ligand interaction. However, the relatively low throughput of current NMR screens and their high demand on sample requirements generally makes it impractical to collect complete binding curves to measure the affinity for each compound in a large and diverse chemical library. As a result, NMR ligand screens are typically limited to identifying candidates that bind to a protein and do not give any estimate of the binding affinity. To address this issue, a methodology has been developed to rank binding affinities for ligands based on NMR screens that use 1D (1)H NMR line-broadening experiments. This method was demonstrated by using it to estimate the dissociation equilibrium constants for twelve ligands with the protein human serum albumin (HSA). The results were found to give good agreement with previous affinities that have been reported for these same ligands with HSA.
Detection of snRNP assembly intermediates in Cajal bodies by fluorescence resonance energy transfer (2004)

Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) are required for pre-mRNA splicing throughout the nucleoplasm, yet snRNPs also concentrate in Cajal bodies (CBs). To address a proposed role of CBs in snRNP assembly, we have used fluorescence resonance energy transfer (FRET) microscopy to investigate the subnuclear distribution of specific snRNP intermediates. Two distinct complexes containing the protein SART3 (p110), required for U4/U6 snRNP assembly, were localized: SART3.U6 snRNP and SART3.U4/U6 snRNP. These complexes segregated to different nuclear compartments, with SART3.U6 snRNPs exclusively in the nucleoplasm and SART3.U4/U6 snRNPs preferentially in CBs. Mutant cells lacking the CB-specific protein coilin and consequently lacking CBs exhibited increased nucleoplasmic levels of SART3.U4/U6 snRNP complexes. Reconstitution of CBs in these cells by expression of exogenous coilin restored accumulation of SART3.U4/U6 snRNP in CBs. Thus, while some U4/U6 snRNP assembly can occur in the nucleoplasm, these data provide evidence that SART3.U6 snRNPs form in the nucleoplasm and translocate to CBs where U4/U6 snRNP assembly occurs.
The synthesis of poly(3,4-dihydroxystyrene) and poly[(sodium 4-styrenesulfonate)-co-(3,4-dihydroxystyrene)] (1998)

Poly(2-methoxy-4-vinylphenol), polyMVP, and poly[(sodium 4-styrenesulfonate)-co-(2-methoxy-4-vinylphenol)], poly(SSS/MVP), were synthesized by radical polymerization using Vazo-64 or tributylborane as initiator. Poly(3,4-dihydroxystyrene) and poly[(sodium 4-styrenesulfonate)-co-(3,4-dihydroxystyrene)] were obtained by demethylation of polyMVP and poly(SSS/MVP) using HBr and trimethylsilyl iodide, respectively. (Co)polymer structures were confirmed by 1H and 13C NMR spectra. About 30 wt.-% gel formed in the polyMVP polymerizations, whereas only a small amount (0.5 mol-%) of gel formed in the copolymerizations.
CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting (2015)

CRISPR/Cas9-based therapeutics hold the possibility for permanent treatment of genetic disease. The potency and specificity of this system has been used to target dominantly inherited conditions caused by heterozygous missense mutations through inclusion of the mutated base in the short-guide RNA (sgRNA) sequence. This research evaluates a novel approach for targeting heterozygous single-nucleotide polymorphisms (SNPs) using CRISPR/Cas9. We determined that a mutation within KRT12, which causes Meesmann's epithelial corneal dystrophy (MECD), leads to the occurrence of a novel protospacer adjacent motif (PAM). We designed an sgRNA complementary to the sequence adjacent to this SNP-derived PAM and evaluated its potency and allele specificity both in vitro and in vivo. This sgRNA was found to be highly effective at reducing the expression of mutant KRT12 mRNA and protein in vitro. To assess its activity in vivo we injected a combined Cas9/sgRNA expression construct into the corneal stroma of a humanized MECD mouse model. Sequence analysis of corneal genomic DNA revealed non-homologous end-joining repair resulting in frame-shifting deletions within the mutant KRT12 allele. This study is the first to demonstrate in vivo gene editing of a heterozygous disease-causing SNP that results in a novel PAM, further highlighting the potential for CRISPR/Cas9-based therapeutics.
Controlled Motion in an Elastic World (1993)

The flexibility of the drives and structures of controlled motion systems are presented as an obstacle to be overcome in the design of high performance motion systems, particularly manipulator arms. The task and the measure of performance to be applied determine the technology appropriate to overcome this obstacle. Included in the technologies proposed are control algorithms (feedback and feedforward), passive damping enhancement, operational strategies, and structural design. Modeling of the distributed, nonlinear system is difficult, and alternative approaches are discussed. The author presents personal perspectives on the history, status and future directions in this area.
Lineage tracing on transcriptional landscapes links state to fate during differentiation (2020)

A challenge in biology is to associate molecular differences among progenitor cells with their capacity to generate mature cell types. Here, we used expressed DNA barcodes to clonally trace transcriptomes over time and applied this to study fate determination in hematopoiesis. We identified states of primed fate potential and located them on a continuous transcriptional landscape. We identified two routes of monocyte differentiation that leave an imprint on mature cells. Analysis of sister cells also revealed cells to have intrinsic fate biases not detectable by single-cell RNA sequencing. Finally, we benchmarked computational methods of dynamic inference from single-cell snapshots, showing that fate choice occurs earlier than is detected by state-of the-art algorithms and that cells progress steadily through pseudotime with precise and consistent dynamics.
Surgical and non-surgical treatment of Achilles Tendon rupture. A prospective randomized study. (1981)

One hundred and five consecutive patients with a closed acute rupture of the tendo achillis were assigned randomly for surgical or non-surgical treatment. After treatment, the patients were evaluated clinically and with static and dynamic measurements of plantar flexion strength. Only minor differences were noted between the final results in the two groups. Non-surgical treatment had the advantages of shorter morbidity and no hospital stay. The frequency of major complications was about the same in both groups of patients: two re-ruptures and two deep infections in patients who had operations as compared with five re-ruptures in the conservatively treated patients. I concluded that non-surgical treatment offers advantages over surgical treatment.
Effectiveness and Cost-Benefit of Influenza Vaccination of Healthy Working Adults (2000)

Influenza vaccination of healthy working adults younger than 65 years can reduce the rates of ILI, lost workdays, and physician visits during years when the vaccine and circulating viruses are similar, but vaccination may not provide overall economic benefits in most years. JAMA. 2000;284:1655-1663.
Adoptive transfer of regulatory NKT lymphocytes ameliorates non‐alcoholic steatohepatitis and glucose intolerance in ob/ob mice and is associated with intrahepatic CD8 trapping (2006)

The aim of this study was to determine the effect of adoptive transfer of regulatory natural killer T (NKT) lymphocytes on the metabolic disorder in leptin-deficient ob/ob mice, which feature depletion and defective function of NKT and CD4 lymphocytes. Leptin-deficient ob/ob mice were subjected to transplantation of 1 x 10(6) of either ob/ob or wild-type-derived NKT lymphocytes, or to transplantation of either ob/ob or wild-type-derived splenocytes. The effect on hepatic fat content was measured by magnetic resonance imaging (signal intensity index) and histology, using the steatohepatitis grading scale. The degree of glucose intolerance was measured by an oral glucose tolerance test (GTT). Adoptive transfer of wild-type or ob/ob-derived regulatory NKT cells led to a 12% decrease in hepatic fat content. A significant histological shift from macrosteatosis to microsteatosis was observed. Marked improvement in the GTT was noted in wild-type or ob/ob-derived NKT recipients. Metabolic effects were associated with a significant decrease in peripheral and intrahepatic CD4/CD8 lymphocyte ratios. Intrahepatic CD8 trapping was observed in all responders. Serum interleukin 10 levels decreased significantly. In conclusion, adoptive transfer of a relatively small number of regulatory NKT lymphocytes into ob/ob mice results in a significant reduction in hepatic fat content, a shift from macro to microsteatosis, and significant improvement in glucose intolerance. These effects were associated with decreased peripheral and intrahepatic CD4/CD8 ratios and decreased interleukin 10 levels. The results further support a role for regulatory NKT lymphocytes in the pathogenesis of non-alcoholic steatohepatitis in the leptin-deficient murine model.
Evaluation of clinical parameters and estrogen receptor alpha gene polymorphisms for patients with endometriosis (2005)

Endometriosis is a chronic inflammatory disease, which is especially found in women with subfertility problems with an incidence of up to 30%. The disease is considered an estrogen-dependent disorder, where DNA polymorphisms of the estrogen receptor alpha (ERalpha) in connection with endometriosis are controversially discussed. From a German population of women, clinical data associated with the disease, including the American Fertility Society (AFS) I-IV classification, and non-clinical parameters were evaluated statistically in endometriosis patients (n = 98) and in control women (n = 98) without endometriosis. Using a multivariate statistical analysis, significant associations of endometriosis with dysmenorrhea (P < 0.001) and allergies against medicaments (P = 0.042) were found. A positive trend between first grade family history of endometriosis and allergies against medicaments was also observed, suggesting a genetic relationship. From both collectives, DNA from peripheral blood was analyzed for the frequency of the ERalpha DNA polymorphisms Xba1 (A/G) and PvuII (T/C) in intron 1 and the ERalpha exonic DNA polymorphism (G229A) with an amino acid exchange (Gly77Ser) in the transactivation domain. DNA samples from endometriosis lesions and control tissues from the same collectives were also analyzed for the exonic G229A polymorphism. Only homozygote wild-type alleles for the polymorphism G229A were found, making it a rare polymorphism in mid-European individuals. Allele types for the PvuII and Xba1 polymorphisms were analyzed with the observed statistically significant clinical parameters and showed no significant association with endometriosis; however a trend with AFS IV was noted, which could contribute to lesion severity. In conclusion, the analyzed polymorphisms in the ERalpha do not have a functional role concerning specific clinical parameters associated with endometriosis.
Auditory attention in the congenitally blind (1998)

Functional reorganization of auditory attention was studied in 12 congenitally blind subjects and 12 controls using high-density event-related potentials during a highly focused dichotic listening task. Reaction times for the attend-ear intensity-deviant targets were markedly faster for the blind. Brain activity associated with sustained attention (N1 effect, Nd), and with the automatic detection of deviants in an unattended channel (MMN), did not exhibit reorganization. In contrast, marked plasticity changes were reflected in late auditory attentional processing (attend-ear targets), in the form of a prolonged negativity (200-450 ms post-stimulus) that was absent in the sighted subjects. The plasticity changes in the blind had a time course indicating progressive recruitment of parietal and then occipital regions, providing new evidence for cross-modal sensory reorganization in the blind.