gebhart/patrepeval huggingface dataset:
The roles of different porcine cytochrome P450 enzymes and cytochrome b5A in skatole metabolism (2012)

Boar taint is the unfavourable odour and taste from pork fat, which results in part from the accumulation of skatole (3-methylindole, 3MI). The key enzymes in skatole metabolism are thought to be cytochrome P450 2E1 (CYP2E1) and cytochrome 2A (CYP2A); however, the cytochrome P450 (CYP450) isoform responsible for the production of the metabolite 6-hydroxy-3-methylindole (6-OH-3MI, 6-hydroxyskatole), which is thought to be involved in the clearance of skatole, has not been established conclusively. The aim of this study was to characterize the role of porcine CYP450s in skatole metabolism by expressing them individually in the human embryonic kidney HEK293-FT cell line. This system eliminates the problems of the lack of specificity of antibodies, inhibitors and substrates for CYP450 isoforms in the pig, and contributions of any other CYP450s that would be present. The results show that pig CYP1A1, CYP2A19, CYP2C33v4, CYP2C49, CYP2E1 and CYP3A and human CYP2E1 (hCYP2E1) are all capable of producing the major skatole metabolite 3-methyloxyindole (3MOI), as well as indole-3-carbinol (I3C), 5-hydroxy-3-methylindole (5-OH-3MI), 6-OH-3MI, 2-aminoacetophenone (2AAP) and 3-hydroxy-3-methyloxindole. CYP2A19 produced the highest amount of the physiologically important metabolite 6-OH-3MI, followed by porcine CYP2E1 and CYP2C49; CYP2A19 also produced more 6-OH-3MI than hCYP2E1. Co-transfection with CYB5A increased the production of skatole metabolites by some of the CYP450s, suggesting that CYB5A plays an important role in the metabolism of skatole. We also show the utility of this expression system to check the specificity of selected substrates and antibodies for porcine CYP450s. Further information regarding the abundance of different CYP450 isoforms is required to fully understand their contribution to skatole metabolism in vivo in the pig.
Gastro-Protective and Anti-Oxidant Potential of Althaea officinalis and Solanum nigrum on Pyloric Ligation/Indomethacin-Induced Ulceration in Rats (2019)

Recently, an alternative disease treatment approach is the research of medicaments from traditional medicine. Plants with anti-oxidant capabilities are used as herbal treatments for ulcer diseases. Medicinal/herbal extracts containing phytoconstituents have significant anti-ulcer activities in in vivo experiments on animal models, compared to reference drugs. The current study aims to inspect gastro-protective as well as in vitro and in vivo anti-oxidant potential of <i>Althaea officinalis</i> and <i>Solanum nigrum</i> extracts on pyloric-ligation/indomethacin-induced gastric-ulceration in rats. Rats were divided into six groups: normal control, gastric ulcer control, two standard pretreatment groups receiving omeprazole and misoprostol, and two test pretreatment groups receiving <i>Althaea officinalis</i> and <i>Solanum nigrum</i>. Pretreatments were administrated orally for 14 days. On the 15th day, animals, excluding the normal control group, were exposed to pyloric-ligation followed by indomethacin injection. After four hours, the rat's stomachs were removed and gastric juice and blood samples were collected. Pyloric-ligation/indomethacin administration caused considerable elevation in ulcer number, ulcer index, acid and pepsin productivity, aggressive factors, and gastric mucosal lipid-peroxide contents. Moreover, reduction in titratable acidity, gastric mucosal nitric-oxide, anti-oxidant contents, and protective factors accompanied gastric-ulceration. Additionally, elevation in pro-inflammatory cytokines content and reduction in cystathionine-β-synthase and heme-oxygenase-1 expression was witnessed. Omeprazole, misoprostol, <i>Althaea officinalis,</i> and <i>Solanum nigrum</i> pretreatments fixed blood and tissue biomarkers, thereby protecting them from pyloric-ligation/indomethacin-induced gastric-ulceration in rats, which is hopeful for clinical examinations.
Presence of Host ICAM-1 in Human Immunodeficiency Virus Type 1 Virions Increases Productive Infection of CD4 + T Lymphocytes by Favoring Cytosolic Delivery of Viral Material (2003)

Although there is now convincing evidence that the infectivity of human immunodeficiency virus type 1 (HIV-1) is increased by incorporation of host intercellular adhesion molecule 1 (ICAM-1) in budding virions, the exact mechanism(s) through which ICAM-1 can so significantly affect HIV-1 biology remains obscure. To address this question, we focused our attention on the most proximal events in the virus life cycle. We made comparative analyses to estimate attachment and internalization of isogenic HIV-1 particles either lacking or bearing host-derived ICAM-1. Using attachment-and-entry assays and confocal fluorescence microscopy, we found that virus binding and uptake were both markedly enhanced by insertion of ICAM-1 within the virus envelope when PM1 lymphoid cells and primary human cells (i.e., peripheral blood lymphocytes and purified CD4(+) T cells) were used as targets. Moreover, ICAM-1-bearing virions entered cells with faster uptake kinetics than viruses devoid of ICAM-1. Experiments conducted with fully competent viruses further confirmed the positive effect of virion-anchored host ICAM-1 on HIV-1 replication. Interestingly, subcellular-fractionation assays revealed that ICAM-1 incorporation modifies the HIV-1 entry route by increasing the level of viral material released in the cytosol, a process of internalization known to be mediated mainly by pH-independent membrane fusion and to result in productive infection. A virion-based fusion assay confirmed that the acquisition of ICAM-1 increases the efficiency of productive HIV-1 entry in primary CD4(+) T lymphocytes. These observations provide new insights into how interactions other than those with gp120 and CD4-coreceptor complex can modulate the process of productive HIV-1 infection in CD4(+) T lymphocytes, a cell target highly relevant to HIV-1 pathogenesis.
XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair (2012)

DNA double strand breaks (DSBs), induced by ionizing radiation (IR) and endogenous stress including replication failure, are the most cytotoxic form of DNA damage. In human cells, most IR-induced DSBs are repaired by the nonhomologous end joining (NHEJ) pathway. One of the most critical steps in NHEJ is ligation of DNA ends by DNA ligase IV (LIG4), which interacts with, and is stabilized by, the scaffolding protein X-ray cross-complementing gene 4 (XRCC4). XRCC4 also interacts with XRCC4-like factor (XLF, also called Cernunnos); yet, XLF has been one of the least mechanistically understood proteins and precisely how XLF functions in NHEJ has been enigmatic. Here, we examine current combined structural and mutational findings that uncover integrated functions of XRCC4 and XLF and reveal their interactions to form long, helical protein filaments suitable to protect and align DSB ends. XLF-XRCC4 provides a global structural scaffold for ligating DSBs without requiring long DNA ends, thus ensuring accurate and efficient ligation and repair. The assembly of these XRCC4-XLF filaments, providing both DNA end protection and alignment, may commit cells to NHEJ with general biological implications for NHEJ and DSB repair processes and their links to cancer predispositions and interventions.
Optical coherence hyperspectral microscopy with a single supercontinuum light source (2021)

In the paper, we have developed an optical coherence hyperspectral microscopy with a single supercontinuum light source. The microscopy consists of optical coherence tomography (OCT) and hyperspectral imaging (HSI), which can visualize the structural and functional characteristics of biological tissues. The 500 to 700 nm band is selected for HSI and OCT imaging, where HSI enables imaging of oxygen saturation and hemoglobin (Hb) content, while OCT acquires structural characteristics to assess the morphology of biological tissues. The system performance of the optical coherence hyperspectral microscopy is verified by normal mice ears, and the practical applications of the microscopy is further performed in 4T1 and inflammation Balb/c mice ears in vivo. The experimental results demonstrate that the microscopy has potential to provide complementary information for clinical applications.
A new class of pressure-sensitive adhesives based on interpolymer and polymer-oligomer complexes (2009)

On the basis of previous concepts concerning the molecular nature of pressure-sensitive adhesion, a simple method of preparing new adhesives with the desired mechanical and adhesive behavior and water-absorbability via mixing of nonadhesive polymers has been developed. Pressure-sensitive adhesion is related to the combination of a high energy of cohesion and a large free volume, which leads to a high molecular mobility. This method is based on the formation of interpolymer or polymer-oligomer complexes during mixing of macromolecules capable of hydrogen, electrostatic, or ionic bonding. In interpolymer complexes, a high cohesion results from the formation of bonds between macromolecules carrying complementary groups in main chains, whereas free volume is related to defectiveness of the resulting network and formation of loops. In complexes formed by a high-molecular-mass polymer and an oligomer carrying complementary reactive groups at ends of short chains, a high energy of cohesion is related to their interaction with mainchain functional groups of the polymer, whereas a relatively large free volume is associated with the length and flexibility of intermacromolecular crosslinks via oligomer chains. The adhesive and viscoelastic properties of adhesives and their water absorbability are regulated by changes in the composition of mixtures of a film-forming polymer with a polymer or oligomer crosslinker and a plasticizer. In this case, an increase in cohesive strength is achieved owing to an increase in the crosslinker concentration, while the enhancement of free volume is ensured by the increasing plasticizer content in the blend. Adhesive materials capable of adherence to wet substrates, hydroactivated adhesives, and adhesion moisture sorbents have been prepared for the first time.
Cannabinoid Receptor Type II Ligands from Sandalwood Oil and Synthetic α-Santalol Derivatives (2023)

Bioassay-guided fractionation of the essential oil of <i>Santalum album</i> led to the identification of α-santalol (<b>1</b>) and β-santalol (<b>2</b>) as new chemotypes of cannabinoid receptor type II (CB<sub>2</sub>) ligands with <i>K</i><sub>i</sub> values of 10.49 and 8.19 μM, respectively. Nine structurally new α-santalol derivatives (<b>4a</b>-<b>4h</b> and <b>5</b>) were synthesized to identify more selective and potent CB<sub>2</sub> ligands. Compound <b>4e</b> with a piperazine structural moiety demonstrated a <i>K</i><sub>i</sub> value of 0.99 μM against CB<sub>2</sub> receptor and did not show binding activity against cannabinoid receptor type I (CB<sub>1</sub>) at 10 μM. Compounds <b>1</b>, <b>2</b>, and <b>4e</b> increased intracellular calcium influx in SH-SY5Y human neuroblastoma cells that were attenuated by CB<sub>2</sub> antagonism or inverse agonism, supporting the results that these compounds are CB<sub>2</sub> agonists. Molecular docking showed that <b>1</b> and <b>4e</b> had similar binding poses, exhibiting a unique interaction with Thr114 within the CB<sub>2</sub> receptor, and that the piperazine structural moiety is required for the binding affinity of <b>4e</b>. A 200 ns molecular dynamics simulation of CB<sub>2</sub> complexed with <b>4e</b> confirmed the stability of the complex. This structural insight lays a foundation to further design and synthesize more potent and selective α-santalol-based CB<sub>2</sub> ligands for drug discovery.
Fluorescence saturation in confocal microscopy (1994)

Summary The effects of fluorescence saturation on imaging in confocal microscopy have been studied. To include saturation it was necessary to deviate from the widely assumed linear relationship between the fluorescence and the illumination intensity. The lateral response for a point‐like object, as well as the optical sectioning power, decreases depending on the degree of saturation. For very high illumination intensities the response for a saturated point object approached that of a conventional fluorescence microscope in which the fluorescence was not saturated. The decrease in the axial confocal response has been confirmed qualitatively by experiment.
Transcatheter Arterial Embolization for Blunt Hepatic Trauma in a Preschooler (2022)

Published reports regarding the use of transcatheter arterial embolization (TAE) for blunt hepatic trauma in young children, especially preschoolers (3–5 years old), are still scarce. We present a case report of a 4-year-old girl who was involved in a motor vehicle accident while sitting in the passenger seat without wearing a seatbelt. Focused Assessment with Sonography for Trauma and contrast-enhanced computed tomography scan showed severe liver injury with signs of active intraabdominal bleeding. Selective hepatic artery embolization was performed to control arterial hemorrhage. No procedure-related complications occurred, and she was discharged on foot on day 14. TAE is a safe and effective treatment for hemostasis in blunt hepatic trauma, and it should be strongly considered as a treatment option not only in adults but in young children as well.
Visual Influences on the Development and Recovery of the Vestibuloocular Reflex in the Chicken (2001)

Whenever the head turns, the vestibuloocular reflex (VOR) produces compensatory eye movements to help stabilize the image of the visual world on the retina. Uncompensated slip of the visual world across the retina results in a gradual change in VOR gain to minimize the image motion. VOR gain changes naturally during normal development and during recovery from neuronal damage. We ask here whether visual slip is necessary for the development of the chicken VOR (as in other species) and whether it is required for the recovery of the VOR after hair cell loss and regeneration. In the first experiment, chickens were reared under stroboscopic illumination, which eliminated visual slip. The horizontal and vertical VORs (h- and vVORs) were measured at different ages and compared with those of chickens reared in normal light. Strobe-rearing prevented the normal development of both h- and vVORs. After 8 wk of strobe-rearing, 3 days of exposure to normal light caused the VORs to recover partially but not to normal values. In the second experiment, 1-wk-old chicks were treated with streptomycin, which destroys most vestibular hair cells and reduces hVOR gain to zero. In birds, vestibular hair cells regenerate so that after 8 wk in normal illumination they appear normal and hVOR gain returns to values that are normal for birds of that age. The treated birds in this study recovered in either normal or stroboscopic illumination. Their hVOR and vVOR and vestibulocollic reflexes (VCR) were measured and compared with those of untreated, age-matched controls at 8 wk posthatch, when hair cell regeneration is known to be complete. As in previous studies, the gain of the VOR decreased immediately to zero after streptomycin treatment. After 8 wk of recovery under normal light, the hVOR was normal, but vVOR gain was less than normal. After 8 wk of recovery under stroboscopic illumination, hVOR gain was less than normal at all frequencies. VCR recovery was not affected by the strobe environment. When streptomycin-treated, strobe-recovered birds were then placed in normal light for 2 days, hVOR gain returned to normal. Taken together, the results of these experiments suggest that continuous visual feedback can adjust VOR gain. In the absence of appropriate visual stimuli, however, there is a default VOR gain and phase to which birds recover or revert, regardless of age. Thus an 8-wk-old chicken raised in a strobe environment from hatch would have the same gain as a streptomycin-treated chicken that recovers in a strobe environment.
Optimal conditions for determination of zinc bacitracin, polymyxin B, oxytetracycline and sulfacetamide in animal feed by micellar electrokinetic capillary chromatography (2008)

A separation technique for zinc bacitracin, polymyxin B, oxytetracycline and sulfacetamide in animal feedstuffs by micellar electrokinetic capillary chromatography (MEKC) was developed. The running buffer was 20 mmol l(-1) borate, 20 mmol l(-1) phosphate, pH 8.4, containing 20 mmol l(-1) sodium dodecylsulphate and 10% (v/v) methanol. MEKC was performed at 25 degrees C; the applied voltage was 25 kV with a running pressure of 10 mbar. Simultaneous UV detection for all analytes was at 215 nm. The method was validated for specificity, accuracy, linearity, precision and robustness. It was shown to be specific, accurate (recoveries were 99.7 +/- 0.3, 99.9 +/- 0.9, 99.8 +/- 1.0 and 99.5 +/- 0.4, respectively, for oxytetracycline-, sulfacetamide-, polymyxin B- and zinc bacitracin-spiked samples of feed for cow, pigs, chicken and cattle), linear over the tested range (correlation coefficients > or =0.9987) and precise (RSDs below 1.8% for each analyte). The method was applied to determine zinc bacitracin, polymyxin B, oxytetracycline and sulfacetamide as additives in animal feed.
LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design (2014)

Abstract Lectins (Ls) play an important role in many diseases such as different types of cancer, parasitic infections and other diseases. Interestingly, the Protein Data Bank (PDB) contains +3000 protein 3D structures with unknown function. Thus, we can in principle, discover new Ls mining non‐annotated structures from PDB or other sources. However, there are no general models to predict new biologically relevant Ls based on 3D chemical structures. We used the MARCH‐INSIDE software to calculate the Markov‐Shannon 3D electrostatic entropy parameters for the complex networks of protein structure of 2200 different protein 3D structures, including 1200 Ls. We have performed a Linear Discriminant Analysis (LDA) using these parameters as inputs in order to seek a new Quantitative Structure‐Activity Relationship (QSAR) model, which is able to discriminate 3D structure of Ls from other proteins. We implemented this predictor in the web server named LECTINPred, freely available at http://bio‐aims.udc.es/LECTINPred.php. This web server showed the following goodness‐of‐fit statistics: Sensitivity=96.7 % (for Ls), Specificity=87.6 % (non‐active proteins), and Accuracy=92.5 % (for all proteins), considering altogether both the training and external prediction series. In mode 2, users can carry out an automatic retrieval of protein structures from PDB. We illustrated the use of this server, in operation mode 1, performing a data mining of PDB. We predicted Ls scores for +2000 proteins with unknown function and selected the top‐scored ones as possible lectins. In operation mode 2, LECTINPred can also upload 3D structural models generated with structure‐prediction tools like LOMETS or PHYRE2. The new Ls are expected to be of relevance as cancer biomarkers or useful in parasite vaccine design.
On the necessity of high performance RF front-ends in broadband wireless access employing multicarrier modulations (OFDM) (2002)

Multicarrier systems of the OFDM-type perform a frequency domain decomposition of a channel characterized by frequency selective distortion in a multitude of subchannels that are affected by frequency flat distortion. The distortion in each independent subchannel can then be compensated by simple gain and phase adjustments, somehow overcoming the need of one of the most complex components of a digital modem: the equalizer. On the other hand, coding and transmission power assignments can be applied across the subchannels in a way that resembles the Shannon water pouring argument. As the bandwidth of the subchannels is made sufficiently small one can asymptotically reach the channel capacity. We prove that a careful implementation of the analog RF front-end is extremely critical to the asymptotic behavior of multicarrier transmission in approaching capacity. In fact multicarrier signals exhibit extreme vulnerability to distortions induced by RF electronics. We concentrate on the characterization of those degradations that can not be compensated at baseband by means of digital signal processing and show that the throughput achievable by realistic OFDM modems is much lower than what typically advertised, particularly in transceivers with low performance analog RF front-end.
Improvement the Conductivity and Flame Retardant Properties of Carboxylated Single-Walled Carbon Nanotube/Cotton Fabrics Using Citric Acid and Sodium Hypophosphite (2017)

Improvement of existing properties and creation of new material properties are the most important reasons for increasing industrial uses of cotton fabrics. In this research work, carboxylated single-walled carbon nanotubes (CSWCNT) were stabilized by different methods on a cotton fabric surface, using citric acid (CA) as a cross-linking agent and sodium hypophosphite (SHP) as a catalyst. A scanning electron microscope, electrical resistivity equipment, reflective spectrophotometer has been applied to investigate the influence of carboxylated single-walled carbon nanotube on the performance of the cotton fabrics. Also the flammability of cotton fabric modified by CSWCNT, CA, and SHP was evaluated by measuring the percentage of char yield. The test results were compared and discussed.
Community Treatment Centers for Isolation of Asymptomatic and Mildly Symptomatic Patients with Coronavirus Disease, South Korea (2020)

As a part of measures to decrease spikes in coronavirus disease (COVID-19) cases and deaths outside of hospitals, the government of South Korea introduced a plan for community treatment centers (CTCs) to isolate and monitor patients with mild COVID-19 symptoms. We assessed outcomes of 568 patients admitted to 3 CTCs near Daegu. More (64.6%) women than men (35.4%) were admitted, and the mean age of patients was 36.0 years (SD +15.0 years). Among all patients, 75.7% remained asymptomatic while at the CTCs. The mean time patients remained at CTCs was 19.6 days (SD +5.8 days) from the day of diagnosis until our study ended on March 23, 2020. Because they offer appropriate clinical triaging and daily monitoring for patients, CTCs are a safe alternative to medical institutions for asymptomatic or mildly symptomatic patients with COVID-19.
CAPACITY PLANNING WITH DEMAND UNCERTAINTY (1997)

ABSTRACT We examine how the ability to augment capacity on an as-needed basis affects capacity planning. If it is feasible and desirable to augment all resources on an as-needed basis, optimal capacity planning can be done separately for each resource. Optimality of this simple rule is lost if even one capacity resource imposes “hard” constraints. Simulations indicate that simplifying capacity planning to focus on an expected bottleneck resource dominates product- or resource-level capacity planning, when all resources impose hard constraints and the firm's product mix problem is significant.
Mechanisms of action for light therapy: A review of molecular interactions (2012)

Five decades after the first documented use of a laser for wound healing, research in light therapy has yet to elucidate the underlying biochemical pathways causing its effects. The aim of this review is to summarize the current research into the biochemical mechanisms of light therapy in order to better direct future studies. The implication of cytochrome c oxidase as the photoacceptor modulating light therapy is reviewed, as are the predominant hypotheses of the biochemical pathways involved in the stimulation of wound healing, cellular proliferation, production of transcription factors and other reported stimulatory effects.