gebhart/patrepeval huggingface dataset:
Expression of the structural proteins of Semliki Forest virus from cloned cDNA microinjected into the nucleus of baby hamster kidney cells. (1982)

The three structural proteins of Semliki Forest virus--i.e., the capsid, p62, and E1 proteins--were expressed in baby hamster kidney cells from cloned DNA transcribed from the virus-specific 4.1-kilobase mRNA. The cDNA was engineered into an expression vector developed by others [Mulligan, R. C. & Berg, P. (1980) Science 209, 1422--1427] downstream from the simian virus 40 early promoter and was introduced into cell nuclei by microneedle injection. Immunofluorescence analysis of injected cells showed that the capsid protein was located in the cell cytoplasm, whereas the membrane proteins were associated with cellular membranes. The p62 protein was shown to be transported from the rough endoplasmic reticulum to the plasma membrane, whereas the E1 protein remained in the rough endoplasmic reticulum.
Plasma Amino Acid Concentrations in 108 Children Receiving a Pediatric Amino Acid Formulation as Part of Parenteral Nutrition (2010)

While most AAs were within the normal range, formulation modifications are needed to normalize free cystine in infants and young children, free tyrosine in all children, and phenylalanine in neonates. The decrease in glutamine concentrations in older children has been noted by our group before, and may imply limited ability to convert glutamic acid to glutamine, or increased consumption of glutamine. In either case, increased concentrations of glutamine in older children, especially those receiving home parenteral nutrition, should be considered.
Issues in transnet packetized voice communication (1977)

In recent years, very important progress was made in both real-time digital computer communication and real-time digital voice communication, due to the growing importance of geographically distributed computation, the growing need for resource sharing, and the need for secure voice communication. The progress in digital voice communication—mainly aimed at low data rate and high fidelity speech communication—has led to various vocoding techniques such as LPC and CVSD. The progress in real-time computer communication—which is mainly aimed at low delays, high bandwidth and high cost-effectiveness—led to technologies such as packet switching, packet-radio, and satellite communication, as well as intercomputer communication protocols. It is the natural result of the progress in both areas that the use of packet switching technology be considered for voice communication. In this paper the issues involved in the application of packet-switching networks to real-time voice communication are identified and explained.
Time Course of Early and Late Changes in Plasma DNA in Trauma Patients (2003)

Plasma DNA concentrations increase early after injury and are higher in patients with severe injuries and in those who develop organ failure. Increased plasma DNA persists for days after injuries, especially in patients with multiple organ dysfunction syndrome.
Structural characterization of human elastin derived peptides containing the GXXP sequence (2005)

The degradation of elastin, the insoluble biopolymer of tropoelastin, can lead to the production of small peptides. These elastin-derived peptides (EDPs) are playing a key role in cellular behavior within the extracellular matrix, showing a great variety of biological effects such as chemotaxis, stimulation of cell proliferation, ion flux modifications, vasorelaxation, and inflammatory enzymes secretion. It has also been demonstrated recently that EDPs containing the GXXPG motif could induce pro-MMP1 and pro-MMP3 upregulation. Elastolysis could then cause collagen degradation and play an important role in the aging process. Many experimental studies have been devoted to EDPs, but their structure/activity relationships are not well elucidated yet. However, the assumption that their active conformation is a type VIII beta-turn on GXXP was highly suggested on the basis of predictive statistical calculations. Investigation of the EDPs three-dimensional (3D) structure would provide useful information for drug-design strategies to propose specific inhibitors. The work presented here reports theoretical results obtained from molecular dynamics simulations performed over 128 human EDPs containing the GXXP motif. We show that all the peptides, for which the central residues are not glycines, adopt a canonical (or very close to) type VIII beta-turn structure on the GXXP sequence. Amino acids surrounding this motif are also important for the structural behavior. Any residue located before the GXXP motif (XGXXP) increases the beta-turn stabilization, whereas the residue located after GXXP (GXXPX) has no significant structural effect. Moreover, we show their biological activity can be correlated with their ability to exhibit a type VIII beta-turn conformation.
Studies in the biochemistry of micro-organisms. 95. Rugulosin, a crystalline colouring matter of Penicillium rugulosum Thom (1955)

Raper & Thom (1949) in their Manual of the Peni- cillia separate species in this genus into four major sections, Monoverticillata, Asymmetrica, Biverti- cillata-Symmetrica and Polyverticillata. They sub- divide each of the sections into a number of series so that the Biverticillata-Symmetrica section, for example, includes six such series among which, for RuGuILosn; Considerable difficulty was experienced in establish- ing the empirical formula for rugulosin. Samples crystallized from ethanol or acetone, in yellow cubes or prisms, and dried to constant weight in high vacuum at 1000 or below, are very hygroscopic.
Evaluation of the activity of a number of antimicrobial agents against mycobacteria within mouse macrophages by a radiomefric method (1993)

[3H]-uridine was incorporated by Mycobacterium bovis BCG with increasing intensity as the incubation period was increased. Rifampicin and isoniazid inhibited incorporation of the label rapidly. Similar inhibition was seen with M. tuberculosis H37Rv and several clinical isolates of M. tuberculosis both in axenic medium and inside macrophages. Ofloxacin and ciprofloxacin were both inhibitory but clofazimine was not. The combination of rifampicin with either isoniazid or ethambutol produced enhanced killing, but the combination of ethambutol and isoniazid was not synergic. Mycobacterium avium-intracellulare isolates from AIDS patients were less susceptible to rifampicin and were unaffected by isoniazid, ethambutol, clofazimine, ofloxacin and ciprofloxacin. The results obtained by inhibition of [3H]-uridine incorporation by intracellular mycobacteria correlated with conventional in-vitro MICs and was reproducible and rapid; a definitive result was obtainable within seven days.
Microthermoforming of microfluidic substrates by soft lithography (µTSL): optimization using design of experiments (2011)

We present a detailed analysis of microthermoforming by soft lithography (μTSL) for replication of foil-based microfluidic substrates. The process was systematically optimized by design of experiments (DOE) enabling fabrication of defect-free lab-on-a-chip devices. After the assessment of typical error patterns we optimized the process toward the minimum deviation between mold and thermoformed foil substrates. The following process parameters have most significant impact on the dimensional responses (p 40% relative impact. The DOE results in an empirical process model with a maximum deviation between the prediction and experimental proof of 2% for the optimum parameter set. Finally, process optimization is validated by the fabrication and testing of a microfluidic structure for blood plasma separation from human whole blood. The optimized process enabled metering of a nominal volume of 4.0 μl of blood plasma with an accuracy deviation of 3% and a metering precision of ±7.0%. The μTSL process takes about 30 min and easily enables the replication of 300 μm wide microchannels having vertical sidewalls without any draft angles in a well-controllable way. It proves to be suitable for multiple applications in the field of microfluidic devices. S Online supplementary data available from stacks.iop.org/JMM/21/115002/mmedia (Some figures in this article are in colour only in the electronic version)
Characterization of an Insecticidal Toxin and Pathogenicity of Pseudomonas taiwanensis against Insects (2014)

Pseudomonas taiwanensis is a broad-host-range entomopathogenic bacterium that exhibits insecticidal activity toward agricultural pests Plutella xylostella, Spodoptera exigua, Spodoptera litura, Trichoplusia ni and Drosophila melanogaster. Oral infection with different concentrations (OD = 0.5 to 2) of wild-type P. taiwanensis resulted in insect mortality rates that were not significantly different (92.7%, 96.4% and 94.5%). The TccC protein, a component of the toxin complex (Tc), plays an essential role in the insecticidal activity of P. taiwanensis. The ΔtccC mutant strain of P. taiwanensis, which has a knockout mutation in the tccC gene, only induced 42.2% mortality in P. xylostella, even at a high bacterial dose (OD = 2.0). TccC protein was cleaved into two fragments, an N-terminal fragment containing an Rhs-like domain and a C-terminal fragment containing a Glt symporter domain and a TraT domain, which might contribute to antioxidative stress activity and defense against macrophagosis, respectively. Interestingly, the primary structure of the C-terminal region of TccC in P. taiwanensis is unique among pathogens. Membrane localization of the C-terminal fragment of TccC was proven by flow cytometry. Sonicated pellets of P. taiwanensis ΔtccC strain had lower toxicity against the Sf9 insect cell line and P. xylostella larvae than the wild type. We also found that infection of Sf9 and LD652Y-5d cell lines with P. taiwanensis induced apoptotic cell death. Further, natural oral infection by P. taiwanensis triggered expression of host programmed cell death-related genes JNK-2 and caspase-3.
Femtosecond laser collagen cross-linking without traditional photosensitizers (2015)

Collagen cross-linking in cornea has the capability of enhancing its mechanical properties and thereby providing an alternative treatment for eye diseases such as keratoconus. Currently, riboflavin assisted UVA light irradiation is a method of choice for cross-link induction in eyes. However, ultrafast pulsed laser interactions may be a powerful alternative enabling in-depth treatment while simultaneously diminishing harmful side effects such as, keratocyte apoptosis. In this study, femtosecond laser is utilized for treatment of bovine cornea slices. It is hypothesized that nonlinear absorption of femtosecond laser pulses plays a major role in the maturation of immature cross-links and the promotion of their growth. Targeted irradiation with tightly focused laser pulses allows for the absence of a photosensitizing agent. Inflation test was conducted on half treated porcine cornea to identify the changes of mechanical properties due to laser treatment. Raman spectroscopy was utilized to study subtle changes in the chemical composition of treated cornea. The effects of treatment are analyzed by observing shifts in Amide I and Amide III bands, which suggest deformation of the collagen structure in cornea due to presence of newly formed cross-links.
Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant (2021)

SARS-CoV-2 Delta variant has rapidly replaced the Alpha variant around the world. The mechanism that drives this global replacement has not been defined. Here we report that Delta spike mutation P681R plays a key role in the Alpha-to-Delta variant replacement. In a replication competition assay, Delta SARS-CoV-2 efficiently outcompeted the Alpha variant in human lung epithelial cells and primary human airway tissues. Delta SARS-CoV-2 bearing the Alpha-spike glycoprotein replicated less efficiently than the wild-type Delta variant, suggesting the importance of Delta spike in enhancing viral replication. The Delta spike has accumulated mutation P681R located at a furin cleavage site that separates the spike 1 (S1) and S2 subunits. Reverting the P681R mutation to wild-type P681 significantly reduced the replication of Delta variant, to a level lower than the Alpha variant. Mechanistically, the Delta P681R mutation enhanced the cleavage of the full-length spike to S1 and S2, leading to increased infection via cell surface entry. In contrast, the Alpha spike also has a mutation at the same amino acid (P681H), but the spike cleavage from purified Alpha virions was reduced compared to the Delta spike. Collectively, our results indicate P681R as a key mutation in enhancing Delta variant replication via increased S1/S2 cleavage. Spike mutations that potentially affect furin cleavage efficiency must be closely monitored for future variant surveillance.
Mechanism for the Enhanced Diffusion of Charged Oxygen Ions inSiO2 (2001)

Based on real-space multigrid electronic structure calculations, we find that a double Si-O-Si bridge structure is the lowest energy configuration of interstitial oxygen ions (O(-) and O(2-)) in SiO2, where two additional Si-O bonds are formed with almost no interaction between the interstitial and host O atoms, while the peroxy linkage is the most stable structure for neutral interstitial O. We propose a diffusion mechanism of interstitial O ions generated from molecular O2 under UV radiation, and find extremely low energy barriers of 0.11--0.27 eV for migration in the form of the double-bridge structure, in good agreement with enhanced oxidation experiments.
An Atomic Clock with 10 –18 Instability (2013)

Atomic clocks have been instrumental in science and technology, leading to innovations such as global positioning, advanced communications, and tests of fundamental constant variation. Timekeeping precision at 1 part in 10(18) enables new timing applications in relativistic geodesy, enhanced Earth- and space-based navigation and telescopy, and new tests of physics beyond the standard model. Here, we describe the development and operation of two optical lattice clocks, both using spin-polarized, ultracold atomic ytterbium. A measurement comparing these systems demonstrates an unprecedented atomic clock instability of 1.6 × 10(-18) after only 7 hours of averaging.
SURFACE BIOLOGY OF DNA BY ATOMIC FORCE MICROSCOPY (2001)

The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.
Seedless, Surfactantless Wet Chemical Synthesis of Silver Nanowires (2003)

We report a method to make crystalline silver nanowires in water, in the absence of a surfactant or polymer to direct nanoparticle growth, and without externally added seed crystallites. The reaction is one in which silver salt is reduced to silver metal, at 100 °C, by sodium citrate, in the presence of NaOH. Hydroxide ion concentration is key to producing nanowires, which are up to 12 microns long, instead of nanospheres.
Treatment of pustular psoriasis with clofazimine (1978)

Two cases of generalized pustular psoriasis (von Zumbusch) were successfully treated with clofazimine. No side effects were noted except deep red staining of the skin which faded afterwards.
Effects of Endogenous PPAR Agonist Nitro-Oleic Acid on Metabolic Syndrome in Obese Zucker Rats (2010)

Nitroalkene derivatives of nitro-oleic acid (OA-NO(2)) are endogenous lipid products with novel signaling properties, particularly the activation of PPARs. The goal of this proposal was to examine the therapeutic potential of this OA-NO(2) in treatment of obesity and obesity-related conditions in obese Zucker rats. The animals were randomly divided to receive OA-NO(2), oleic acid (OA), both at 7.5 mug/kg/d, or vehicle ethanol via osmotic mini-pumps for 2 weeks. Following OA-NO(2) treatment, food intake was decreased as early as the first day and this effect appeared to persist throughout the experimental period. At day 14, body weight gain was significantly reduced by OA-NO(2) treatment. This treatment significantly reduced plasma triglyceride and almost normalized plasma free fatty acid and significantly increased plasma high-density lipid (HDL). The plasma TBARS and proteinuria were paralelly decreased. In contrast, none of these parameters were affected by OA treatment. After 14 days of OA-NO(2) treatment, hematocrit, a surrogate of fluid retention associated with PPARgamma agonists, remained unchanged. Together, these data demonstrated that OA-NO(2) may offer an effective and safe therapeutic intervention for obesity and obesity-related conditions.
<i>Clostridium difficile</i> Toxins: Mediators of Inflammation (2012)

Clostridium difficile is a significant problem in hospital settings as the most common cause of nosocomial diarrhea worldwide. C. difficile infections (CDIs) are characterized by an acute intestinal inflammatory response with neutrophil infiltration. These symptoms are primarily caused by the glucosylating toxins, TcdA and TcdB. In the past decade, the frequency and severity of CDIs have increased markedly due to the emergence of so-called hypervirulent strains that overproduce cytotoxic glucosylating toxins relative to historical strains. In addition, these strains produce a third toxin, binary toxin or C. difficile transferase (CDT), that may contribute to hypervirulence. Both the glucosylating toxins and CDT covalently modify target cell proteins to cause disassembly of the actin cytoskeleton and induce severe inflammation. This review summarizes our current knowledge of the mechanisms by which glucosylating toxins and CDT disrupt target cell function, alter host physiology and stimulate immune responses.
THE USE OF NEGATIVE PRESSURE UNDER SKIN FLAPS AFTER RADICAL MASTECTOMY (1952)

Syracuse, New York THE DEPARTMENT OF SURGERY, STATE UNIVERSITY OF NEW YORK, COLLEGE OF MEDICINE, SYRACUSE, NEW YORK
Input-Output Structure and the General Equilibrium Dynamics of Inflation and Output (2000)

An antiserum, obtained by immunising rabbits with a human peptide-protein conjugate, was shown to inhibit histamine release from rat mast cells both in vitro and in vivo. Immunisation of sensitised rats with the same peptide reduced IgE antibody formation and serum histamine concentration, and abolished systemic anaphylactic reactions in response to allergen challenge. This peptide may form the basis of a vaccine in a new approach to the immunotherapy of atopic disease.
Improved Method of 5,10,15,20-Tetrakis(4-hydroxyphenyl)porphyrins Synthesis (2013)

porphyrin were synthesized in the 3 solvents mixture by Adler-Longo method. The porphyrin purification was carried out by ethyl acetate extraction.
Anharmonic Phonon Lifetimes in Semiconductors from Density-Functional Perturbation Theory (1995)

The anharmonic lifetimes of zone-center optical phonons in C, Si, and Ge are calculated along with their temperature and pressure dependences, using third-order density-functional perturbation theory. Our basic ingredients are by-products of a standard linear-response calculation of phonon dispersions in the harmonic approximation, resulting in a similarly good agreement with experiments. The microscopic mechanisms responsible for the decay are revealed and shown to be different for different materials and to depend sensitively on the applied pressure.
Determination of Human Coronary Artery Composition by Raman Spectroscopy (1997)

The chemical composition of coronary artery can be quantified accurately with Raman spectroscopy. This opens the possibility of using histochemical analysis to predict acute events such as plaque rupture, to follow the progression of disease, and to select appropriate therapeutic interventions.
Stressor Exposure Disrupts Commensal Microbial Populations in the Intestines and Leads to Increased Colonization by Citrobacter rodentium (2010)

The gastrointestinal tract is colonized by an enormous array of microbes that are known to have many beneficial effects on the host. Previous studies have indicated that stressor exposure can disrupt the stability of the intestinal microbiota, but the extent of these changes, as well as the effects on enteric infection, has not been well characterized. In order to examine the ability of stressors to induce changes in the gut microbiota, we exposed mice to a prolonged restraint stressor and then characterized microbial populations in the intestines using both traditional culture techniques and bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Exposure to the stressor led to an overgrowth of facultatively anaerobic microbiota while at the same time significantly reducing microbial richness and diversity in the ceca of stressed mice. Some of these effects could be explained by a stressor-induced reduction in the relative abundance of bacteria in the family Porphyromonadaceae. To determine whether these alterations would lead to increased pathogen colonization, stressed mice, as well as nonstressed controls, were challenged orally with the enteric murine pathogen Citrobacter rodentium. Exposure to the restraint stressor led to a significant increase in C. rodentium colonization over that in nonstressed control mice. The increased colonization was associated with increased tumor necrosis factor alpha (TNF-alpha) gene expression in colonic tissue. Together, these data demonstrate that a prolonged stressor can significantly change the composition of the intestinal microbiota and suggest that this disruption of the microbiota increases susceptibility to an enteric pathogen.