gebhart/patrepeval huggingface dataset:
Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species (2014)

We conclude the following: 1) genomes of Nocardia strains carry as many PKS-I and NRPS gene clusters as those of Streptomyces strains, 2) the number of PKS-I and NRPS gene clusters in Nocardia strains varies substantially depending on species, and N. brasiliensis strains carry the largest numbers of clusters among the species studied, 3) the seven Nocardia strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied, and 4) different N. brasiliensis strains have some different gene clusters of PKS-I/NRPS, although the rest of the clusters are common within the N. brasiliensis strains. Genome sequencing suggested that Nocardia strains are highly promising resources in the search of novel secondary metabolites.
Antifungal Activity of Gepinacin Scaffold Glycosylphosphatidylinositol Anchor Biosynthesis Inhibitors with Improved Metabolic Stability (2020)

The glycosylphosphatidylinositol anchor biosynthesis inhibitor gepinacin demonstrates broad-spectrum antifungal activity and negligible mammalian toxicity in culture but is metabolically labile. The stability and bioactivity of 39 analogs were tested <i>in vitro</i> to identify LCUT-8, a stabilized lead with increased potency and promising single-dose pharmacokinetics. Unfortunately, no antifungal activity was seen at the maximum dosing achievable in a neutropenic rabbit model. Nevertheless, structure-activity relationships identified here suggest strategies to further improve compound potency, solubility, and stability.
Expression and localization of the multidrug resistance-associated protein 3 in rat small and large intestine (2002)

Multidrug resistance-associated protein 3 (MRP3; symbol ABCC3), has been shown to mediate ATP-dependent transport of organic anions including 17beta-glucuronosyl estradiol, glucuronosyl bilirubin, monovalent, and sulfated bile salts. MRP3 mRNA expression was reported in rat intestine suggesting a role of MRP3 in the intestinal transport. We examined the expression and localization of MRP3 in rat small and large intestine by RT-PCR, immunofluorescence, and immunoblot analysis. MRP3 was identified in all intestinal segments by RT-PCR. MRP3 expression was low in duodenum and jejunum but markedly increased in ileum and colon. With the use of a rat MRP3 specific antibody, MRP3 was localized to the basolateral domains of enterocytes. Immunofluorescence analysis and immunoblot analysis confirmed a strong expression of rat MRP3 in ileum and colon. In contrast, MRP2 was predominantly expressed in the proximal segments of rat small intestine. Our findings demonstrate a high expression of rat MRP3 in ileum and colon and provide evidence for an involvement of MRP3 in the ATP-dependent transport of organic anions, including bile salts from the enterocyte into blood.
Local Overexpression of Monocyte Chemoattractant Protein-1 at Vessel Wall Induces Infiltration of Macrophages and Formation of Atherosclerotic Lesion (2002)

Monocyte/macrophage infiltration to the arterial wall is an initial step in atherosclerosis, and monocyte chemoattractant protein-1 (MCP-1) is thought to play a central role in the recruitment of these cells. In the present study, we examined the role of local expression of MCP-1 at the vessel wall in the initiation and development of atherosclerosis. We transfected the cDNA encoding rat MCP-1 into the vessel wall of the rabbit carotid artery with the use of the hemagglutinating virus of Japan (HVJ)-liposome method. The rabbits were divided into the following groups: (1) those fed normal chow and transfected with MCP-1-HVJ, (2) those fed a high cholesterol diet (1% cholesterol) and transfected with MCP-1-HVJ, and (3) those fed a high cholesterol diet and transfected with control-HVJ. Prescribed diets were started 2 weeks before transfection and were continued for another 2 weeks. In group 1, vascular lesion formation was not found, and anti-rabbit monocyte/macrophage antibody (RAM-11) staining for monocytes/macrophages was negative, although anti-rat MCP-1 antibody (R-17) staining for rat MCP-1 was positive mainly in endothelial cells. Cholesterol feeding increased plasma cholesterol levels to 1801+/-444 mg/dL in group 2. In group 2, all rabbits displayed neointimal formation with infiltration of RAM-11-positive cells, and a part of the lesion was also positive for Sudan III lipid staining. In group 3, hypercholesterolemia did not induce the infiltration of monocytes/macrophages and subsequent lesion formation in the vessel wall despite definite upregulation of intercellular adhesion molecule-1 and vascular cell adhesion molecule-1 on the endothelium. To initiate atherosclerotic changes, local MCP-1 overexpression at the vessel is not sufficient, and activation of other factors induced by hypercholesterolemia is required.
Polarization Aberrations In The Solar Activity Measurements Experiments (SAMEX) Solar Vector Magnetograph (1989)

An optical design and polarization analysis of the Air Force/NASA Solar Activity Measurements Experiments solar vector magnetograph optical system is performed. Polarization aberration theory demonstrates that conventional telescope coating designs introduce unacceptably high levels of polarization aberrations into the optical system. Several ultralow polarization mirror and lens coatings designs for this instrument are discussed. Balancing of polarization aberrations at different surfaces is demonstrated.
Antibiotics from basidiomycetes. XI. The biological activity of siccayne, isolated from the marine fungus Halocyphina villosa J.&E. Kohlmeyer. (1981)

From submerged cultures of the marine basidiomycete Halocyphina villosa we isolated siccayne (4-(2,4-dihydroxyphenyl)-2-methyl-1-buten-3-yne) (1), a metabolite first described from fermentations of the deuteromycete Helminthosporium siccans. Siccayne is a moderately active antibiotic, which inhibits Gram-positive bacteria and some fungi at concentrations of 10 approximately 50 micrograms/ml. Its cytotoxic effect is much more pronounced on both normal and Rous-sarcoma-virus transformed chicken embryo fibroblasts as compared to cells of the Ehrlich ascites carcinoma. Siccayne apparently interferes with the uptake of nucleoside precursors into eucaryotic cells as well as with the in vitro incorporation of nucleotides into DNA and RNA.
Bioelectric Characterization of Epithelia from Neonatal CFTR Knockout Ferrets (2013)

Cystic fibrosis (CF) is a life-shortening, recessive, multiorgan genetic disorder caused by the loss of CF transmembrane conductance regulator (CFTR) chloride channel function found in many types of epithelia. Animal models that recapitulate the human disease phenotype are critical to understanding pathophysiology in CF and developing therapies. CFTR knockout ferrets manifest many of the phenotypes observed in the human disease, including lung infections, pancreatic disease and diabetes, liver disease, malnutrition, and meconium ileus. In the present study, we have characterized abnormalities in the bioelectric properties of the trachea, stomach, intestine, and gallbladder of newborn CF ferrets. Short-circuit current (ISC) analysis of CF and wild-type (WT) tracheas revealed the following similarities and differences: (1) amiloride-sensitive sodium currents were similar between genotypes; (2) responses to 4,4'-diisothiocyano-2,2'-stilbene disulphonic acid were 3.3-fold greater in CF animals, suggesting elevated baseline chloride transport through non-CFTR channels in a subset of CF animals; and (3) a lack of 3-isobutyl-1-methylxanthine (IBMX)/forskolin-stimulated and N-(2-Naphthalenyl)-((3,5-dibromo-2,4-dihydroxyphenyl)methylene)glycine hydrazide (GlyH-101)-inhibited currents in CF animals due to the lack of CFTR. CFTR mRNA was present throughout all levels of the WT ferret and IBMX/forskolin-inducible ISC was only observed in WT animals. However, despite the lack of CFTR function in the knockout ferret, the luminal pH of the CF ferret gallbladder, stomach, and intestines was not significantly changed relative to WT. The WT stomach and gallbladder exhibited significantly enhanced IBMX/forskolin ISC responses and inhibition by GlyH-101 relative to CF samples. These findings demonstrate that multiple organs affected by disease in the CF ferret have bioelectric abnormalities consistent with the lack of cAMP-mediated chloride transport.
Scalable Optimal Flexibility Control, modeling and estimation of commercial buildings (2020)

The rapid penetration of uncertain and unpredictable renewable energy resources into the power grid has made generation planning and real-time power balancing a challenge, thus rendering demand side advanced control a necessity. In this work, we introduce field validation of a distributed optimization framework for load flexibility control in the grid where aggregated power of multiple loads follow a commanded ancillary service power. The proposed scheme is a model predictive control (MPC) approach where the pertaining large scale optimization problem is solved in a distributed fashion based on Newton iteration to provide fast convergence, and is scalable to large numbers of loads at the aggregation level [1]. The target load is a campus comprising commercial buildings. We introduce a simplified model of a complex commercial building heating, ventilation, and air conditioning (HVAC) system to achieve observability given limited available measurements. Moreover, the simplified model makes the modeling and estimation scalable in the sense that it can be applied to different buildings with minimal adjustments. We demonstrate the performance of estimator and MPC controller via closed-loop control of a commercial building on the Navy Yard campus in Philadelphia to track a commanded power while comfort measures are kept within acceptable range. It is shown that the estimator tracks output measurements well while parameters stay relatively constant and the optimizer converges in real-time. The paper is an introductory step for optimal building control with the purpose of providing grid ancillary services. It introduces a scalable approach from the perspective of modeling, estimation and distributed optimization implementing MPC on an aggregation of multiple commercial buildings. While the candidate distributed energy resource (DER) is a commercial building, the novel MPC approach is not restricted to buildings; rather, it is designed to be applicable to general large scale heterogeneous loads, as outlined in [1].
Neutralizing antibodies elicited in rabbits by patient-derived Env trimer immunization (2012)

Methods Based on in-vitro neutralizing activity in serum, patients (n=6, subtype A and B infected) were selected and Env sequences of early HIV-1 variants, still sensitive to autologous neutralization, were used to generate soluble Env as immunogens. Gp140 trimeric proteins were expressed (293T cells) and purified. Rabbits (4/group) were immunized s.c. at weeks 0, 2, 4, 8 with 100μg trimer adjuvanted with cationic CAF01. Control groups received 20μg and 100μg trimer plus/minus CAF01 respectively. Sera collected at weeks 0, 2, 4, 8, 12 and 14 were screened in gp120-IIIB ELISA and IgG was analyzed in the TZMbl neutralization assay.
Internal Thermal Management of IBM P-Server Large Format Multi-Chip Modules Utilizing Small Gap Technology (2005)

The large Multi-Chip Modules (MCM) used in the IBM p-Server computer systems, and their predecessors, have required rather unique cooling solutions and module hardware designs in order to meet the thermal, mechanical and reliability requirements placed on the package. The module internal thermal solution has evolved from a spring-loaded metal contact technology to a thermal compound based design using a novel gap adjustment technology employing a soldered conduction component. This current MCM makes use of a novel technology called Small Gap Technology (SGT). This technique makes it possible to control thermal compound interface thicknesses or gaps to a very tight tolerance from chip-to-chip and module-to-module. Heat flux values that have been handled vary from approximately 20 to 53 W/cm2 depending on the type of chip and the system performance level. Even higher heat fluxes have been projected for next generation products. The hardware and processing techniques employed to manufacture these modules are quite unique. These products are typically on the order of 100mm chip carrier size or 140mm overall module footprint on a side (approximately 90 cm2 of carrier area) and contain 8 chips and numerous discrete devices. The process fixturing and equipment must be able to handle the relatively large thermal mass of the components. The sequence of processing steps must take into account limitations on the material properties of the various module components. This paper will describe the SGT thermal management solution. The hardware and process employed to make the gap adjustments and the thermal interface material used in these high heat flux applications will be discussed. In addition, supporting thermal/mechanical modelling, thermal performance data and reliability data will be presented.
Slow Cooperative Folding of a Small Globular Protein HPr (1998)

The folding of an 85-residue protein, the histidine-containing phosphocarrier protein HPr, has been studied using a variety of techniques including DSC, CD, ANS fluorescence, and NMR spectroscopy. In both kinetic and equilibrium experiments the unfolding of HPr can be adequately described as a two-state process which does not involve the accumulation of intermediates. Thermodynamic characterization of the native and the transition states has been achieved from both equilibrium and kinetic experiments. The heat capacity change from the denatured state to the transition state (3. 2 kJ mol-1 K-1) is half of the heat capacity difference between the native and denatured states (6.3 kJ mol-1 K-1), while the solvent accessibility of the transition state (0.36) indicates that its compactness is closer to that of the native than that of the denatured state. The high value for the change in heat capacity upon unfolding results in the observation of cold denaturation at moderate denaturant concentrations. Refolding from high denaturant concentrations is, however, slow. The rate constant of folding in water, (14.9 s-1), is small compared to that reported for other proteins of similar size under similar conditions. This indicates that very fast refolding is not a universal character of small globular proteins which fold in the absence of detectable intermediates.
Flip-chip bonding on 6-μm pitch using thin-film microspring technology (2002)

Bonding-pad densities on high-performance integrated-circuit chips are beginning to exceed the limits of available interconnect technologies. Also, stresses due to thermal mismatch in flip-chipped packages are reducing time to contact failure. We have addressed both of these problems by microlithographically fabricating highly elastic cantilever springs in linear arrays on pitches down to 6 /spl mu/m. We have soldered test arrays of 52 springs on this pitch to Si chips with 100% contact yield and good solder wetting to every spring. The fine-pitch capability also facilitates off-chip routing; the very high compliance of the springs should avoid thermal fatigue; and the low thermal conductance along the springs should allow fast-cycle soldering of chips to multichip modules as well as replacement of chips subsequently testing faulty.
Oxidation of the cysteine-rich regions of parkin perturbs its E3 ligase activity and contributes to protein aggregation (2011)

These findings show that oxidative stress alters parkin E3 ligase activity, leading to dysfunction of the ubiquitin-proteasome system and potentially contributing to LB formation.
Supplementary Table 5 from Cyclin G1 Is a Target of miR-122a, a MicroRNA Frequently Down-regulated in Human Hepatocellular Carcinoma (2023)

Supplementary Table 5 from Cyclin G1 Is a Target of miR-122a, a MicroRNA Frequently Down-regulated in Human Hepatocellular Carcinoma
Improvement in Renal Function and Bone Mineral Density after a Switch from Tenofovir/Emtricitabine plus Ritonavir-Boosted Protease Inhibitor to Raltegravir plus Nevirapine: A Pilot Study (2015)

Switching virologically suppressed patients from tenofovir/emtricitabine plus one r/PI to raltegravir plus nevirapine after 48 weeks significantly improved proximal tubular function, increased BMD and reduced serum markers of bone turnover.
Coexistence and Spectrum Sharing Above 100 GHz (2023)

The electromagnetic spectrum plays a fundamental role in the development of the digital society. It enables wireless communications (either between humans or machines) and sensing (for example, for Earth exploration, radio astronomy, imaging, and radars). While each of these uses benefits from a larger bandwidth, the spectrum is a finite resource. This introduces competing interests among the different stakeholders of the spectrum, which have led—so far—to rigid policies and spectrum allocations. Recently, the spectrum crunch in the sub-6-GHz bands has prompted communication technologies to move to higher carrier frequencies, where future sixth-generation (6G) wireless networks can exploit theoretically very large bandwidths. However, the spectrum above 100 GHz features several narrow, yet numerous subbands that are exclusively allocated for passive sensing applications, e.g., for climate and weather monitoring. This prevents the allocation of large contiguous bands to active users of the spectrum, either being communications (which need tens of gigahertz of bandwidth to target terabit-per-second links) or radars. This article explores how spectrum policy and spectrum technologies can evolve to enable <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sharing</i> among different stakeholders in the above 100-GHz spectrum, without introducing harmful interference or disrupting either security applications or fundamental science exploration. This portion of the spectrum presents new challenges and opportunities for the design of spectrum sharing schemes, including higher spreading and absorption losses, extremely directional antenna technologies, and ultrahigh data-rate communications, among others. This article provides a tutorial on current regulations above 100 GHz and highlights how sharing is central to allowing each stakeholder to make the most out of this spectrum. It then defines—through detailed simulations based on standard International Telecommunications Union (ITU) channel and antenna models—scenarios in which active users may introduce harmful interference to passive sensing. Based on this evaluation, it reviews a number of promising techniques that can enable active/passive sharing above 100 GHz. The critical review and tutorial on policy and technologies of this article have the potential to kickstart future research and regulations that promote safe coexistence between active and passive users above 100 GHz, further benefiting the development of digital technologies and scientific exploration.
Development of dyes/tracers for the analysis of different kidney functions. (2022)

GFR is till date the most used parameter for diagnosing kidney diseases. Nevertheless, tubular secretion and reabsorption play an equally important role in healthy functioning of the kidney. The primary focus of this study is to synthesise novel fluorescent markers for evaluating the three physiological processes of the kidney. This would help diagnosing function-/location-specific abnormality in kidney. Since the ideal goal would be to measure all the kidney parameters altogether using a transcutaneous device, the absorbance and emission wavelength for each marker is designed to be significantly different. This paves way for a wholesome, rapid, and non-invasive technique for kidney diagnosis.
Detection of prostate cancer on histopathology using color fractals and Probabilistic Pairwise Markov models (2011)

In this paper we present a system for detecting regions of carcinoma of the prostate (CaP) in H&E stained radical prostatectomy specimens using the color fractal dimension. Color textural information is known to be a valuable characteristic to distinguish CaP from benign tissue. In addition to color information, we know that cancer tends to form contiguous regions. Our system leverages the color staining information of histology as well as spatial dependencies. The color and textural information is first captured using color fractal dimension. To incorporate spatial dependencies, we combine the probability map constructed via color fractal dimension with a novel Markov prior called the Probabilistic Pairwise Markov Model (PPMM). To demonstrate the capability of this CaP detection system, we applied the algorithm to 27 radical prostatectomy specimens from 10 patients. A per pixel evaluation was conducted with ground truth provided by an expert pathologist using only the color fractal feature first, yielding an area under the receiver operator characteristic curve (AUC) curve of 0.790. In conjunction with a Markov prior, the resultant color fractal dimension + Markov random field (MRF) classifier yielded an AUC of 0.831.
Maintenance of improvement in spinal mobility, physical function and quality of life in patients with ankylosing spondylitis after 5 years in a clinical trial of adalimumab (2014)

Clinicaltrials.gov; https://clinicaltrials.gov/NCT00085644.
The Use of Additive Manufacturing for Fabrication of Multi-Function Small Satellite Structures (2013)

The use of small satellites in constellations is limited only by the growing functionality of smallsats themselves. Additive manufacturing provides exciting new design opportunities for development of multifunction CubeSat structures that integrate such functions as propulsion and thermal control into the satellite structures themselves. Manufacturing of these complex multifunction structures is now possible in lightweight, high strength, materials such as titanium by using existing electron beam melting additive manufacturing processes. However, the use of today’s additive manufacturing capabilities is often cost-prohibitive for small companies due to the large capital investments required. To alleviate this impediment the U.S. Department of Energy has established a Manufacturing Demonstration Facility (MDF) at their Oak Ridge National Laboratory (ORNL) in Tennessee that provides industry access to a broad range of energy-efficient additive manufacturing equipment for collaborative use by both small and large organizations. This paper presents a notional CubeSat multifunction design that integrates the propulsion system into a three-unit CubeSat structure. The full-scale structure has been designed and fabricated at the ORNL MDF. The use of additive manufacturing for spacecraft fabrication is opening up many new possibilities in design and fabrication capabilities for what had previously been impossible structures to fabricate.