gebhart/patrepeval huggingface dataset:
An introduction to protein moonlighting (2014)

Moonlighting proteins comprise a class of multifunctional proteins in which a single polypeptide chain performs multiple physiologically relevant biochemical or biophysical functions. Almost 300 proteins have been found to moonlight. The known examples of moonlighting proteins include diverse types of proteins, including receptors, enzymes, transcription factors, adhesins and scaffolds, and different combinations of functions are observed. Moonlighting proteins are expressed throughout the evolutionary tree and function in many different biochemical pathways. Some moonlighting proteins can perform both functions simultaneously, but for others, the protein's function changes in response to changes in the environment. The diverse examples of moonlighting proteins already identified, and the potential benefits moonlighting proteins might provide to the organism, such as through coordinating cellular activities, suggest that many more moonlighting proteins are likely to be found. Continuing studies of the structures and functions of moonlighting proteins will aid in predicting the functions of proteins identified through genome sequencing projects, in interpreting results from proteomics experiments, in understanding how different biochemical pathways interact in systems biology, in annotating protein sequence and structure databases, in studies of protein evolution and in the design of proteins with novel functions.
Fabrication of PLGA nanoparticles with a fluidic nanoprecipitation system (2010)

Particle size is a key feature in determining performance of nanoparticles as drug carriers because it influences circulating half-life, cellular uptake and biodistribution. Because the size of particles has such a major impact on their performance, the uniformity of the particle population is also a significant factor. Particles comprised of the polymer poly(lactic-co-glycolic acid) (PLGA) are widely studied as therapeutic delivery vehicles because they are biodegradable and biocompatible. In fact, microparticles comprised of PLGA are already approved for drug delivery. Unfortunately, PLGA nanoparticles prepared by conventional methods usually lack uniformity. We developed a novel Fluidic NanoPrecipitation System (FNPS) to fabricate highly uniform PLGA particles. Several parameters can be fine-tuned to generate particles of various sizes.
Hierarchical Text-Conditional Image Generation with CLIP Latents (2022)

Contrastive models like CLIP have been shown to learn robust representations of images that capture both semantics and style. To leverage these representations for image generation, we propose a two-stage model: a prior that generates a CLIP image embedding given a text caption, and a decoder that generates an image conditioned on the image embedding. We show that explicitly generating image representations improves image diversity with minimal loss in photorealism and caption similarity. Our decoders conditioned on image representations can also produce variations of an image that preserve both its semantics and style, while varying the non-essential details absent from the image representation. Moreover, the joint embedding space of CLIP enables language-guided image manipulations in a zero-shot fashion. We use diffusion models for the decoder and experiment with both autoregressive and diffusion models for the prior, finding that the latter are computationally more efficient and produce higher-quality samples.
Ascorbic acid deficiency impairs wound healing in surgical patients: Four case reports (2016)

Vitamin C or ascorbic acid (AA) is the antiscorbutic factor preventing scurvy. It is essential for collagen synthesis, serving as cofactor in the enzymatic conversion of procollagen into collagen. Scurvy is regarded as something from the past; however, patients with low or subclinical levels of AA are frequently seen in our hospital. A subclinical deficiency will not often cause the display of the hallmark symptoms of scurvy, but this may lead to an altered collagen synthesis and have major implications for adequate wound healing, such as in the surgical field. AA was measured by HPLC using UV detection (Recipe) in a teaching hospital surgical patient group (n = 180) within a week pre- or post-surgery. Over a period of 21 months we found AA levels below the reference limit (25 umol/L) in 65 out of 180 patients (36%). Four patients described in detail initially showed poor wound healing. Their AA levels were 8, 4, and 19 umol/L respectively. After starting supplementation (1000 mg/day) a dramatic and fast recovery of extensive and complicated wounds was observed by patients and their clinician. Supplementation was ceased after the wounds were completely healed. AA deficiency is not uncommon in the hospital population, especially in those at risk. Treating deficient patients with AA leads to swift improvement of the wound healing process post-surgery, thereby reducing the costs of extensive wound treatment and extended stay in hospital.
<i>Pax</i> Genes and Neural Tube Defects in the Mouse (2007)

The Pax genes encode a family of transcription factors that are expressed in restricted regions of the developing embryo. Several Pax genes are expressed in the developing nervous system where they are believed to regulate the morphogenesis of neural structures. Loss-of-function mutations in the Pax-3 gene have been identified in a number of alleles of the mouse mutant splotch. In homozygous splotch embryos closure of the neural tube is defective with embryos exhibiting spina bifida and/or exencephaly. Other structures in which Pax-3 is expressed are also affected, most notably those tissues derived from the neural crest and somites.
The outcome of severe closed head injury (1991)

✓ The outcome of severe head injury was prospectively studied in patients enrolled in the Traumatic Coma Data Bank (TCDB) during the 45-month period from January 1, 1984, through September 30, 1987. Data were collected on 1030 consecutive patients admitted with severe head injury (defined as a Glasgow Coma Scale (GCS) score of 8 or less following nonsurgical resuscitation). Of these, 284 either were brain-dead on admission or had a gunshot wound to the brain. Patients in these two groups were excluded, leaving 746 patients available for this analysis. The overall mortality rate for the 746 patients was 36%, determined at 6 months postinjury. As expected, the mortality rate progressively decreased from 76% in patients with a postresuscitation GCS score of 3 to approximately 18% for patients with a GCS score of 6, 7, or 8. Among the patients with nonsurgical lesions (overall mortality rate, 31%), the mortality rate was higher in those having an increased likelihood of elevated intracranial pressure as assessed by a new classification of head injury based on the computerized tomography findings. In the 276 patients undergoing craniotomy, the mortality rate was 39%. Half of the patients with acute subdural hematomas died — a substantial improvement over results in previous reports. Outcome differences between the four TCDB centers were small and were, in part, explicable by differences in patient age and the type and severity of injury. This study describes head injury outcome in four selected head-injury centers. It indicates that a mortality rate of approximately 35% is to be expected in such patients admitted to experienced neurosurgical units.
An optimal wavelet thresholding method for speckle noise reduction (1996)

This paper proposes a method using optimal thresholding of wavelet coefficients for speckle reduction. Our approach minimizes the difference between the standard deviations of the estimated and removed noise.
Determination of Single-Cell Oxygen Consumption with Impedance Feedback for Control of Sample−Probe Separation (2005)

The ability to measure chemical gradients surrounding single cells provides novel insights into several areas of cell dynamics--particularly metabolism. Detection of metabolic oxygen consumption can be achieved from a single mammalian cell using a modulated amperometric sensor in a self-referencing mode. To date, however, apart from visual cues, we do not have a reliable and cell-compatible method for determining and stabilizing the position of such probes. In this paper, we report on having successfully measured the increase in the uncompensated resistance of an electrochemical cell upon approach to single, living, biological cells, while simultaneously measuring the metabolic oxygen consumption. This was accomplished by applying an ac and a dc excitation signal to the electrode. The applied ac waveform was a 100-kHz sine wave with an amplitude of 10 mV rms, while the dc voltage applied was -600 mV. The two signals were shown not to interfere with one another. Furthermore, it is shown that the sample-probe distance can be measured for approach to single cells on the order of 10-15-microm diameter and 5-microm height, with 100-nm resolution.
Differential Stimulation of Cholesterol and Unsaturated Fatty Acid Biosynthesis in Cells Expressing Individual Nuclear Sterol Regulatory Element-binding Proteins (1998)

Three sterol regulatory element-binding proteins (SREBP-1a, -1c, and -2) stimulate transcription of genes involved in synthesis and receptor-mediated uptake of cholesterol and fatty acids. Here, we explore the individual roles of each SREBP by preparing lines of Chinese hamster ovary (CHO) cells that express graded amounts of nuclear forms of each SREBP (designated nSREBPs) under control of a muristerone-inducible nuclear receptor system. The parental hamster cell line (M19 cells) lacks its own nSREBPs, owing to a deletion in the gene encoding the Site-2 protease, which releases nSREBPs from cell membranes. By varying the concentration of muristerone, we obtained graded expression of individual nSREBPs in the range that restored lipid synthesis to near physiologic levels. The results show that nSREBP-2 produces a higher ratio of synthesis of cholesterol over fatty acids than does nSREBP-1a. This is due in part to a selective ability of low levels of nSREBP-2, but not nSREBP-1a, to activate the promoter for squalene synthase. nSREBP-1a and -2 both activate transcription of the genes encoding stearoyl-CoA desaturase-1 and -2, thereby markedly enhancing the production of monounsaturated fatty acids. nSREBP-1c was inactive in stimulating any transcription at the concentrations achieved in these studies. The current data support the emerging view that the nSREBPs act in complementary ways to modulate the lipid composition of cell membranes.
200, 400 and 800 GHz Schottky diode "substrateless" multipliers: design and results (2002)

Several sub-millimeter doubler circuits have been designed and built using a new fabrication technology. To reduce the RF losses in the passive circuitry, the substrate under the transmission lines is etched away, leaving the metal suspended in air held by its edges on a GaAs frame. This allows the circuit to be handled and mounted easily, and makes it very robust. To demonstrate this technology, broadband balanced planar doublers have been built and tested at 400 GHz. The next generation 200, 400 and 800 GHz doublers with improved performance are also discussed. The 368-424 GHz circuits were measured and achieved 20% efficiency at 387 GHz. The 3 dB bandwidth of the fix-tuned doubler is around 9%. The maximum output power measured is around 8 mW and drops down to 1 mW at 417 GHz. This represents the highest frequency waveguide based planar doubler to date in the literature.
Supported Ionic Liquid Enzymatic Catalysis for the Production of Biodiesel (2007)

Abstract Pseudomonas cepacia lipase supported in the 1‐ n ‐butyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid is an alternative “green” method for the production of biodiesel from the alcoholysis of soybean oil. The transesterification reaction catalyzed by this ionic liquid‐supported enzyme can be performed at room temperature, in the presence of water and without the use of organic solvents. It is also compatible with various alcohols (including isoamyl alcohol). The biodiesel is separated by simple decantation and the recovered ionic liquid/enzyme catalytic system can be re‐used at least four times without loss of catalytic activity and selectivity.
A cobalt catalyst for reductive etherification of 5-hydroxymethyl-furfural to 2,5-bis(methoxymethyl)furan under mild conditions (2018)

Conversion of platform molecule 5-hydroxymethylfurfural (HMF) into high-value-added derivatives has attracted significant interest.
CMOS integrated silicon pressure sensor (1987)

The sensor described includes a four-arm piezoresistance bridge circuit, an amplifier, and a bridge excitation circuit. This circuit is used to stabilize changes in sensitivity due to variations in temperature and supply voltage. The sensor was fabricated using a self-aligned double-poly Si gate p-well CMOS process combined with an electrochemical etch-stop technique using N/SUB 2/H/SUB 4/-H/SUB 2/O anisotropic etchant for the thin-square diaphragm formation. The silicon wafer was electrostatically adhered to a glass plate to minimize thermally induced stress. Less than a /spl plusmn/0.5% sensitivity shift and less than a /spl plusmn/5-mV offset shift were obtained in the 0-70/spl deg/C range, with a 1-V/kg/cm/SUP 2/ pressure sensitivity. By using a novel excitation technique, a sensitivity change of less than /spl plusmn/1.5% under a /spl plusmn/10% supply voltage variation was also achieved.
New Method and Reagents in Organic Synthesis. 87. Reaction of Trimethylsilyldiazomethane with Quinones (1990)

Reaction of trimethylsilyldiazomethane with various quinones affords indazoles 2 , 2-substituted 3-trimethylsilyimethyl-1 , 4quinones 3, siiylcyclopropanes 4 , and trimethylsilylmethylenedioxy derivatives 5, depending upon substrates.We have already reported2 that most of reactions of trimethylsilyldi$zomethane (TMSCHN2) with various olefins in the presence or absence of metal salt catalysts give siiylcyclopropanes.As an extension of this work, we now wish to report the reaction of TMSCHN2 with quinones, which gives various products 2-5, depending upon substrates.
Ultrafiltration efficiency during automated peritoneal dialysis using glucose-based solutions. (2008)

The ultrafiltration (UF) efficiency of peritoneal dialysis (PD) solutions, defined as the net UF divided by the amount of carbohydrate absorbed per dwell, has been shown to be higher during long dwells with 7.5% icodextrin solution (Extraneal: Baxter Healthcare Corporation, Deerfield, IL, U.S.A.) than during those with glucose-based solution (2.5% and 4.25% Dianeal: Baxter Healthcare Corporation), prompting a better understanding of UF efficiency. We used the three-pore kinetic model of PD transport to investigate UF efficiency for single long dwells and various combinations of multiple short glucose-based dwells during automated PD (APD). To demonstrate a practical consequence of the effect of dwell time, we simulated two hypothetical APD prescriptions (A and B) in which fluid with a high glucose concentration was used during either the long day dwell (A: 4.25%; B: 2.5%) or the short night dwells (A: 3 x 1.5% + 1 x 2.5%; B: 4 x 2.5%). Computer simulations showed that higher glucose concentrations and shorter dwell times increase the UF efficiency of a single dwell, and UF efficiency depends on patient transport status. When 24-hour APD therapy was simulated for a low-average transporter, the net UF did not differ considerably (A: 1132 mL; B: 1154 mL), but total carbohydrate absorption was higher when solution with a high glucose concentration was used during the single long dwell (A: 146 g; B: 137 g), resulting in lower UF efficiency (A: 7.8 mL/g; B: 8.4 mL/g). We conclude that the UF efficiency of the entire regimen should be considered in prescribing PD therapy. When available, Extraneal provides the best UF efficiency during long dwells. Our simulations suggest that raising the glucose concentration in the short dwells and lowering it in the long dwell is the optimal strategy to maximize UF efficiency during APD when Extraneal is not available.
Binding of Rat and Human Surfactant Proteins A and D to<i>Aspergillus fumigatus</i>Conidia (1999)

Surfactant proteins A (SP-A) and D (SP-D) are thought to play important roles in pulmonary host defense. We investigated the interactions of rat and human SP-A and SP-D with Aspergillus fumigatus conidia. Rat SP-D but not rat SP-A bound the conidia, and the binding was inhibited by EDTA, mannose, glucose, maltose, and inositol. Binding studies using a mutant recombinant rat SP-D with altered carbohydrate recognition but normal structural organization clearly established a role for the carbohydrate recognition domain in binding to conidia. However, neither rat SP-A nor SP-D increased the association of fluorescein isothiocyanate-labeled conidia with rat alveolar macrophages as determined by flow cytometry. Both human SP-A (isolated from normal and alveolar proteinosis lungs) and SP-D (recombinant protein and protein isolated from alveolar proteinosis lungs) bound the conidia. These data indicate that important differences exist between rat and human SP-A in binding to certain fungi. Human SP-A and SP-D binding to conidia was also examined in the presence of hydrophobic surfactant components (HSC), containing both the phospholipid and hydrophobic proteins of surfactant. We found that HSC inhibited but did not eliminate human SP-A binding to Aspergillus conidia. In contrast, the SP-D binding to conidia was unaffected by HSC. These findings indicate that SP-D plays a major role in the recognition of Aspergillus conidia in alveolar fluid.
Properties of fetal and adult red blood cell arginase: a possible prenatal diagnostic test for arginase deficiency. (1980)

Prenatal diagnosis of inborn errors of metabolism has been possible only if the enzyme affected is expressed in amniotic fluid cells grown in culture. Arginase is essentially undetectable in normal human fibroblasts, amniotic fluid, and amniotic fluid cells but is present in high amounts in red blood cells. It is absent in the red blood cells of patients with liver arginase deficiency. The properties of the enzyme in the red cells of healthy children and adults were compared to those of the enzyme obtained from cord blood red cells of 13--20-week fetuses obtained at hysterotomy. The activities, heavy metal requirements, heat stability, pH optimum, kinetic properties, and reaction with anti-arginase antibody were examined. Both enzyme species were either identical or substantially similar by all criteria. The adult and fetal enzymes are, therefore, probably determined by the same structural gene. Fetal red cells obtained during amniocentesis and amnioscopy should then be a suitable tissue to use to make the prenatal diagnosis of arginase deficiency.
Clean energy new deal for a sustainable world: from non-CO2 generating energy sources to greener electrochemical storage devices (2011)

The fundamental challenge of the 21st century that mankind has to face is definitely energy supply, its storage and conversion in a way that necessarily protects the environment. For 250 years, the tremendous development of humanity has been founded on the harnessing of fossil fuels (coal, crude oil then natural gas) as primary energy due to their high energy density values and the easiness of access. However, this global pattern of energy supply and use is unsustainable. Global warming and finite fossil-fuel supplies call for a radical change in the energy mix to favour renewable energy sources. Without being exhaustive, we tackle in this article the tricky energy question and associated environmental issues as personally perceived. The eminent role of electric energy produced from decarbonized sources in a future sustainable economy is particularly highlighted as well as the issues of its needed storage. The possible and foreseen hindrances of electrochemical energy storage devices, focusing on the lithium-ion technology, are presented in parallel with the possible pathways to make such a technology greener in synergy with the rise of a biomass-based industry.
Thermal magnetic noise and spectra in spin valve heads (2002)

In this article we present a quantitative micromagnetic modeling analysis of thermally activated magnetic noise in spin valves heads at deep submicron track widths. It is found that, for these spin valve heads, the thermal magnetic noise is at a magnitude that is comparable to that of the head’s Johnson noise. Reducing the sensor track width by keeping the same aspect ratio and film layer thickness will not necessarily yield an increase of thermal magnetic noise, which is attributed to the accompanying increase of the demagnetization field within the sensing layer. However, both the magnitude of noise and the noise spectra are strong functions of the sensor stripe height. An excessive stripe height will yield significantly higher thermal magnetic noise.
It's All Done with Mirrors: Calibration-and-Correspondence-Free 3D Reconstruction (2009)

We describe a 3-D object reconstruction method using a stationary camera and a planar mirror. No external calibration is required. The mirror provides the extra views needed for a multiple-view reconstruction. We examine the imaging geometry of the camera-mirror setup and prove a theorem that gives us the constraints for computing the orientation of the mirror. The constraints are derived from the convex hull of the silhouettes of the images of the object and its mirror reflection. The distance between the mirror and the camera can be then obtained by a single object point or a pair of points on the mirror. After the pose of the mirror is determined, we have multiple calibrated views of the object. We present are construction method customized for the special imaging geometry.
Gene targeting for somatic cell manipulation: rapid analysis of reduced chromosome hybrids by <i>Alu</i>-PCR fingerprinting and chromosome painting (1992)

The techniques of reverse genetics rely heavily on parasexual methods for manipulating the human genome. However, the application of somatic cell genetics is severely limited by the availability of suitable endogenous selectable markers in the genome. We have addressed this problem by targeting a universally selectable marker into a predetermined region of the genome, using a stringent selection for homologous recombination. Correct gene targeting to human chromosome 7q11 was screened for by Southern blotting and confirmed by fluorescent in situ hybridization. Reduced chromosome 7 hybrids were generated by chromosome mediated gene transfer and selection for the neo gene. The resultant transgenomes were characterized by a combination of L1 fingerprinting, locus specific marker analysis, Alu-PCR and chromosome 'painting'. Alu-PCR and L1 'fingerprints' are complementary and mutually consistent. Chromosome 'painting' reflects and extends the results obtained for specific marker co-transfer. Thus Alu-PCR 'fingerprinting' and 'painting' combine to rapidly provide an accurate picture of transgenome content and complexity. Gene targeting, chromosome tagging and subsequent isolation can be applied to any region of the genome for which a molecular probe is available.