gebhart/patrepeval huggingface dataset:
Modulating the activity of short arginine-tryptophan containing antibacterial peptides with N-terminal metallocenoyl groups (2012)

A series of small synthetic arginine and tryptophan containing peptides was prepared and analyzed for their antibacterial activity. The effect of N-terminal substitution with metallocenoyl groups such as ferrocene (FcCO) and ruthenocene (RcCO) was investigated. Antibacterial activity in different media, growth inhibition, and killing kinetics of the most active peptides were determined. The toxicity of selected derivatives was determined against erythrocytes and three human cancer cell lines. It was shown that the replacement of an N-terminal arginine residue with a metallocenoyl moiety modulates the activity of WRWRW-peptides against Gram-positive and Gram-negative bacteria. MIC values of 2-6 µM for RcCO-W(RW)(2) and 1-11 µM for (RW)(3) were determined. Interestingly, W(RW)(2)-peptides derivatized with ferrocene were significantly less active than those derivatized with ruthenocene which have similar structural but different electronic properties, suggesting a major influence of the latter. The high activities observed for the RcCO-W(RW)(2)- and (RW)(3)-peptides led to an investigation of the origin of activity of these peptides using several important activity-related parameters. Firstly, killing kinetics of the RcCO-W(RW)(2)-peptide versus killing kinetics of the (RW)(3) derivative showed faster reduction of the colony forming units for the RcCO-W(RW)(2)-peptide, although MIC values indicated higher activity for the (RW)(3)-peptide. This was confirmed by growth inhibition studies. Secondly, hemolysis studies revealed that both peptides did not lead to significant destruction of erythrocytes, even up to 500 µg/mL for (RW)(3) and 250 µg/mL for RcCO-W(RW)(2). In addition, toxicity against three human cancer cell lines (HepG2, HT29, MCF7) showed that the (RW)(3)-peptide had an IC(50) value of ~140 µM and the RcW(RW)(2) one of ~90 µM, indicating a potentially interesting therapeutic window. Both the killing kinetics and growth inhibition studies presented in this work point to a membrane-based mode of action for these two peptides, each having different kinetic parameters.
Altering the speed of a DNA packaging motor from bacteriophage T4 (2017)

The speed at which a molecular motor operates is critically important for the survival of a virus or an organism but very little is known about the underlying mechanisms. Tailed bacteriophage T4 employs one of the fastest and most powerful packaging motors, a pentamer of gp17 that translocates DNA at a rate of up to ∼2000-bp/s. We hypothesize, guided by structural and genetic analyses, that a unique hydrophobic environment in the catalytic space of gp17-adenosine triphosphatase (ATPase) determines the rate at which the 'lytic water' molecule is activated and OH- nucleophile is generated, in turn determining the speed of the motor. We tested this hypothesis by identifying two hydrophobic amino acids, M195 and F259, in the catalytic space of gp17-ATPase that are in a position to modulate motor speed. Combinatorial mutagenesis demonstrated that hydrophobic substitutions were tolerated but polar or charged substitutions resulted in null or cold-sensitive/small-plaque phenotypes. Quantitative biochemical and single-molecule analyses showed that the mutant motors exhibited 1.8- to 2.5-fold lower rate of ATP hydrolysis, 2.5- to 4.5-fold lower DNA packaging velocity, and required an activator protein, gp16 for rapid firing of ATPases. These studies uncover a speed control mechanism that might allow selection of motors with optimal performance for organisms' survival.
Supplementary Figure 1 from Efficacy of IGFBP7 for treatment of metastatic melanoma and other cancers in mouse models and human cell lines (2023)

Supplementary Figure 1 from Efficacy of IGFBP7 for treatment of metastatic melanoma and other cancers in mouse models and human cell lines
ChemInform Abstract: Total Synthesis of Amphotericin B. Part 3. The Final Stages. (1988)

Abstract The successful strategy for the completion of the synthesis of the title compound involves the preparation of the trichloroacetimidate (IV).
An Intrinsic Flame‐Retardant Organic Electrolyte for Safe Lithium‐Sulfur Batteries (2018)

Safety concerns pose a significant challenge for the large-scale employment of lithium-sulfur batteries. Extremely flammable conventional electrolytes and dendritic lithium deposition cause severe safety issues. Now, an intrinsic flame-retardant (IFR) electrolyte is presented consisting of 1.1 m lithium bis(fluorosulfonyl)imide in a solvent mixture of flame-retardant triethyl phosphate and high flashpoint solvent 1,1,2,2-tetrafluoroethyl-2,2,3,3-tetrafluoropropyl (1:3, v/v) for safe lithium-sulfur (Li-S) batteries. This electrolyte exhibits favorable flame-retardant properties and high reversibility of the lithium metal anode (Coulombic efficiency >99 %). This IFR electrolyte enables stable lithium plating/stripping behavior with micro-sized and dense-packing lithium deposition at high temperatures. When coupled with a sulfurized pyrolyzed poly(acrylonitrile) cathode, Li-S batteries deliver a high composite capacity (840.1 mAh g<sup>-1</sup> ) and high sulfur utilization of 95.6 %.
Comprehensive genomic analyses of a metastatic colon cancer to the lung by whole exome sequencing and gene expression analysis (2013)

We performed whole exome sequencing and gene expression analysis on a metastatic colon cancer to the lung, along with the adjacent normal tissue of the lung. Whole exome sequencing uncovered 71 high-confidence non‑synonymous mutations. We selected 16 mutation candidates, and 13 out of 16 mutations were validated by targeted deep sequencing using the Ion Torrent PGM customized AmpliSeq panel. By integrating mutation, copy number and gene expression microarray data, we identified a JAZF1 mutation with a gain-of-copy, suggesting its oncogenic potential for the lung metastasis from colon cancer. Our pathway analyses showed that the identified mutations closely reflected characteristics of the metastatic site (lung) while mRNA gene expression patterns kept genetic information of its primary tumor (colon). The most significant gene expression network was the 'Colorectal Cancer Metastasis Signaling', containing 6 (ADCY2, ADCY9, APC, GNB5, K-ras and LRP6) out of the 71 mutated genes. Some of these mutated genes (ADCY9, ADCY2, GNB5, K-ras, HDAC6 and ARHGEF17) also belong to the 'Phospholipase C Signaling' network, which suggests that this pathway and its mutated genes may contribute to a lung metastasis from colon cancer.
ADAMTS‐13 content of plasma‐derived factor VIII/ von Willebrand factor concentrates (2014)

To the editor: We read with interest the article by Peyvandi et al. 1 on the ADAMTS-13 content of plasma-derived factor VIII/von Willebrand factor (FVIII/ VWF) concentrates. The authors make reference to published case studies on the use of two FVIII concentrates in treatment of congenital thrombotic thrombocytopenic purpura (TTP): 8Y® 2 and Koate® -DVI 3. Use of 8Y® in the treatment of congenital TTP has also been described by Lester et al. 4 and is exemplified in national guidelines on the diagnosis and management of TTP and other thrombotic microangiopathies 5. In the course of their discussion, the authors compare the ADAMTS-13 activity of Koate®-DVI and 8Y®: 9.08 U/mL and 3.5 U/mL, respectively 6. When these concentrates were utilized in the treatment of congenital TTP, dosing has been described in terms of FVIII administered; 30–35 IU FVIII/kg body weight (b.w.) in the case of KOATE®-DVI 3 and 15–30 IU FVIII/kg b.w. in the case of 8Y® 2. Based on the reported levels of ADAMTS-13 in these two FVIII concentrates, the authors suggest that the ADAMTS-13 administered when 8Y® was given would have been substantially lower than that when Koate® -DVI was used for treatment. However, there is a four-fold difference between the stated FVIII potency of Koate®-DVI (100 IU/mL) and that of 8Y® (25 IU/mL). Taking this potency difference into consideration, the ratio of ADAMTS-13 activity to FVIII in the two products is calculated to be similar at 0.09 U ADAMTS-13/IU FVIII (for Koate®-DVI) and 0.14 U ADAMTS-13/IU FVIII (for 8Y®). This comparison would indicate that, in fact, the dosing regimens described for the two FVIII concentrates would have resulted in similar levels of ADAMTS-13 being administered (2–4 U ADAMTS-13/kg b.w.). Although both these concentrates contain VWF and FVIII, which could influence the clinical outcome, the similarity of these dosing calculations is consistent with a therapeutic mechanism which is mediated by ADAMTS-13 substitution. We agree that VWF multimer distribution in the concentrates is predominantly attributable to manufacturing process rather than to ADAMTS-13 activity. Furthermore, a higher ratio of ADAMTS-13 to FVIII in the concentrate would be consistent with the treatment of a thrombotic condition such as TTP, where elevation of superfluous procoagulant proteins may be undesirable. Sarah Kingsland* Peter Feldman Research, Development and Medical Department, Bio Products Laboratory Ltd., Hertfordshire, United Kingdom
Synthesis and antibacterial activity of copolymers having a quaternary ammonium salt side group (1989)

Abstract Copolymers with a quaternary ammonium salt side group have been prepared from vinylbenzyl–cetyldimethylammonium chloride and acrylonitrile and their antibacterial activity has been examined with Bacillus subtilis, Staphylococcus aureus , and Escherichia coli . Growth inhibitory effect has been found to increase with the increase in the quaternary ammonium salt concentration in the copolymer. The effect is small on gram‐negative bacteria and large on gram‐positive bacteria.
Doping by metal-mediated epitaxy: Growth of As delta-doped Si through a Pb monolayer (2001)

In molecular-beam epitaxy a monolayer of Pb on the Si(111) surface induces single-crystal growth at temperatures well below those required for similar growth on a bare surface. We demonstrate that the suppression of dopant segregation at the lower temperatures attainable by Pb-mediated growth allows the incorporation of As donors at concentrations reaching a few atomic percent. When Pb and Si are deposited on an As-terminated Si(111) substrate at 350 °C, the Pb segregates to the surface without doping the Si film while the As is buried within nanometers of the substrate–film interface. The resulting concentration of electrically active As, 1.8×1021 cm−3, represents the highest concentration of As donors achieved by any delta-doping or thin-film deposition method.
The α-Subunit of the Na+/K+-ATPase has Catalytic Activity Independent of the ß-subunit (1994)

A functional Na+/K+-ATPase enzyme consists of two polypeptides: a large catalytic α-subunit and a smaller glycosylated ß-subunit. Although all catalytic properties of the Na+/K+-ATPase are associated with the α-subunit, it has never been determined if this subunit has activity independent of the ß-subunit. Using the baculovirus expression system we have previously demonstrated that when expressed alone, the rodent α-subunit exists in a stable conformation unassociated with other proteins in the infected Sf-9 cell (3). Here we show that the α-subunit has catalytic activity independent of the ß-subunit. This ATPase activity is dependent on Mg2+, does not require Na+ or K+, and is not inhibited by ouabain. However, the independent α-subunit ATPase activity is inhibited by EGTA, vanadate and increasing ionic strength. The inhibition of the ATPase activity by EGTA is not abolished by the addition of Ca2+ suggesting that EGTA inhibits activity in a manner other than its ion-binding abilities. Phosphorylated intermediates of the independent α-subunit were acid-stable and alkaline-labile, as well as sensitive to hydroxylamine, strongly suggesting the presence of an acylphosphate and thus phosphorylation at an aspartate residue. The physiological role, if any, of this independent α-subunit activity is unknown.
In vitro tooth cleaning efficacy of electric toothbrushes around brackets (2010)

This in vitro study assessed the cleaning efficacy of different electric toothbrushes around upper incisor brackets. Standard and Mini Diamond brackets were fixed on black-stained teeth. The teeth were coated with white titanium oxide and brushed in a machine twice for 1 minute each. Twelve different brush heads with either a wiping or an oscillating-rotating action were tested. After brushing, the teeth were scanned, the black surfaces were assessed planimetrically and a modified plaque index for orthodontic patients (PIOP) was introduced. Tooth areas, which were black again after brushing indicated tooth surface contact of the filaments and were expressed as a percentage of total area. The remaining white areas around the brackets indicated 'plaque-retentive' niches. Analysis of variance was used for individual comparison of the brush types. Bonferroni/Dunn adjustment was applied for multiple testing. The Sonicare toothbrush handle with the brush head 'Compact ProResults' (81.7 per cent) and the brush head 'Standard ProResults' (80.8 per cent), as well as the sonic Waterpik toothbrush SR 800E with the standard brush head (78.2 per cent), showed statistically significantly better cleaning efficacy than all others. The poorest cleaning efficacy was observed for the oscillating-rotating Braun Oral-B Professional Care with the brush head 'Ortho' (less than 50 per cent). The planimetric findings were in correspondence with the results of the PIOP assessment. Cleaning efficacy of electric toothbrushes around brackets on upper incisors was different between the tested brushes. The PIOP was practicable, effective, and easy to use, although it has to be verified in a clinical study.
35 GHz rectifying antenna for wireless power transmission (2007)

A new rectifying antenna for 35 GHz wireless power transmission is presented. The rectifying antenna (rectenna) is designed on R/T Duroid 5880 substrate with ɛr=2.2 and thickness of 1.3 mm. The rectenna arrays are built by series-connecting single elements for higher DC output. The single element, the 1×2 array, and the 2×2 array achieve RF-to-DC conversion efficiencies of 35% when the power density is 30 mW/cm2, corresponding to DC voltages of 0.45, 0.93 and 1.73 V, respectively. The linearity of the rectenna is good, hence it can be used as the building block to assemble a large rectifying antenna array with predictable output performance.
Real-world efficacy of bone modifying agents (BMAs) in patients with breast cancer (BC) treated in an academic health system: Use of the “green button. (2019)

e18054 Background: BC patients (pts) have a high incidence of bone metastases (mets) and associated morbidity. BMAs – zoledronic acid (ZA) and denosumab (Den) – reduce bone met related skeletal related events (SREs). ASCO guidelines do not recommend one over another, and survival and real-world outcome data to guide point-of-care decision-making is lacking. We used the previously developed “Green Button” informatics consult service, designed to rapidly test hypotheses when no applicable published data is available to guide treatment choices (Longhurst et al Health Affairs 2014), to compare BMA efficacy in BC patients. Methods: Patients treated for BC at Stanford HealthCare between 2009 - 2018, receiving standard of care cancer and BMA therapy, as determined by their oncologists, were identified who had &gt; 2 electronic health records (EHRs) documenting BMA administration, and had either ICD9 174 or ICD10 C50 diagnostic codes. Pts were grouped into Den only, ZA only, or both. Two outcomes were analyzed: 1) SREs as a composite outcome of pathologic fracture (1st ICD10 M84.5); spinal cord compression (1st ICD10 M47.1 or G95.2), radiation therapy (1st CPT 77300) or hypercalcemia (calcium ≥10.5); and 2) death. Effects were compared relative to baseline treatment with ZA; we show results of log rank tests for differences in survival outcomes. Three analyses were performed: 1) Unadjusted analysis; 2) Basic matching analysis accounting for length of medical record, age, sex and year of treatment; 3) Propensity score matching using all available data; all prior to index treatment with either Den or ZA. Results: 802 patients had ≥ 2 records of BMA administration. Comparison of Den only and ZA only pts is shown in the table below. Median ages and length of medical record were balanced in all groups. Conclusions: This preliminary retrospective analysis of unsupervised BMA use suggests that Den is superior to ZA for the outcomes of interest; confirmatory analyses are underway.[Table: see text]
Corrinoid Adenosyltransferases (2011)

Abstract ATP corrinoid adenosyltransferase (ACA) enzymes catalyze the transfer of the adenosyl moiety from ATP to cob(I)alamin, resulting in the formation of the unique organometallic C–Co bond characteristic of coenzyme B 12 (adenosylcobalamin, AdoCbl). In the last decade, our knowledge of how these enzymes catalyze the adenosylation of cobalamin has grown rapidly. ACA enzymes also facilitate the thermodynamically unfavorable reduction of cob(II)alamin. Studies with ACA enzymes revealed an unprecedented four‐coordinate square‐planar corrinoid conformation. ACA enzymes bring the reduction potential of cob(II)alamin to within physiological range by generating the four‐coordinate Co(II) corrinoid species. Recently, visual evidence of the existence of a Co(II) corrinoid species was obtained when the 3D crystal structure of the human‐type ACA enzyme was solved with ATP and cob(II)alamin bound in the active site. To date, three types of ACA enzymes have been identified, CobA, PduO, and EutT. The PduO‐type is the most widely distributed ACA enzyme and is the form found in humans where ACA enzymes play an essential role in metabolism; malfunctioning of this enzyme cause severe health defects. Detailed analyses of the catalytic mechanism of ACA enzymes have provided an understanding of how some mutations in the human ACA enzyme render it inactive.
A Wireless Physiological Signal Monitoring System with Integrated Bluetooth and WiFi Technologies (2005)

This paper proposes a wireless patient monitoring system which integrates Bluetooth and WiFi wireless technologies. A wireless portable multi-parameter device was designated to acquire physiological signals and transmit them to a local server via Bluetooth wireless technology. Four kinds of monitor units were designed to communicate via the WiFi wireless technology, including a local monitor unit, a control center, mobile devices (personal digital assistant; PDA), and a web page. The use of various monitor units is intending to meet different medical requirements for different medical personnel. This system was demonstrated to promote the mobility and flexibility for both the patients and the medical personnel, which further improves the quality of health care.
An Error in Determination of Photoinduced Electron Transfer Rates in Langmuir-Blodgett Films (1998)

Abstract In Langmuir-Blodgett (LB) films consisting of viologen (V2+)-pyrene (Py) dyads, the accumulation of viologen cation radical (V+·) was observed during UV irradiation under N2. The additional quenching due to energy transfer by the colored V+· resulted in an error in determination of photoinduced electron transfer rates between the V2+ and Py moieties in the LB films. This type of error can be generally expected in LB films and self-assembled monolayers.
The Role of Resectional Surgery for the Treatment of Localized Multi-drug Resistant Pulmonary Tuberculosis (2000)

Background Surgery may have a role when medical treatment alone is not successful in patients with multi-drug resistant (MDR) pulmonary tuberculosis (PTB). To document the role of resection in MDR PTB, we analyzed 4 years of our experience. Methods A retrospective review was performed on thirteen patients that underwent pulmonary resection for MDR PTB between May 1996 and February 2000. All patients had organisms resistant to many of the first-line drugs including isoniazid (INH) and rifampicin (RFP). Results The thirteen patients were 37.5±12.4 years old (mean±S.D.)(M:F=5:8), and their sputum was culture positive even with adequate medication for prolonged periods (109.7±132.0 months), resistant to 2-8 drugs including isoniazid and rifampin. All patients had localized lesion(s) and most (92.3%) had cavities. At least 3 sensitive anti-TB medications were started before surgery in all patients according to the drug sensitivity test. The preoperative FE1 was 2.37±0.83 L. Lobectomy was performed in 11 patients and pleuropneumonectomy in two. Postoperative mortality did not occur, but pneumonia occurred as a complication in one (7.7%). After 41.5±58.9 days (range 1~150 days) follow up, negative conversion of sputum culture was achieved in all patients within 5 months. Only one patient (7.7%) recurred 32 months after lung resection. Conclusion When medical treatment alone is not successful, surgical resection can be a good treatment option in patients with localized MDR PTB.
Effect of mitogen-activated protein kinase signal transduction pathway on multidrug resistance induced by vincristine in gastric cancer cell line MGC803 (2004)

This study shows that the expression of P-gp can be induced by transient exposure to VCR and this induction can be prevented by PD098059, which can block the activity of MAPK. MAPK signal transduction pathway may play some roles in modulating MDR1 expression in gastric cancer.
Investigation of the biofilm composition. (2017)

&lt;p&gt;A) Effect of enzyme treatment. &lt;i&gt;C&lt;/i&gt;. &lt;i&gt;ljungdahlii&lt;/i&gt; biofilms were grown in well plates by adding 200 mM NaCl to the medium. After 2 days of incubation, the supernatant of all wells was removed and the biofilms were washed twice with PBS buffer. PBS buffer without (control 1) or with 0.2 mg·mL&lt;sup&gt;-1&lt;/sup&gt; proteinaseK or reaction buffer (10 mM Tris HCl pH 7.5, 2.5 mM MgCl&lt;sub&gt;2&lt;/sub&gt;, 0.5 mM CaCl&lt;sub&gt;2&lt;/sub&gt;) without (control 2) or with 2 U·mL&lt;sup&gt;-1&lt;/sup&gt; DNaseI was added to the wells (n = 3). After one hour of enzyme treatment at 37°C, the crystal violet assay (described in text) was performed. B) Confocal laser scanning microscopy images of component-specific stained &lt;i&gt;C&lt;/i&gt;. &lt;i&gt;ljungdahlii&lt;/i&gt; biofilms. &lt;i&gt;C&lt;/i&gt;. &lt;i&gt;ljungdahlii&lt;/i&gt; was grown in chamber slides with the addition of 200 mM NaCl to the medium and, after 2 days of incubation, the biofilms were stained as described in the text with SYPRO ruby red biofilm matrix stain (left) or calcofluor white (right). The scale bars are 50 μm long.&lt;/p&gt;
Reactive Coupling of 4-Vinylaniline with Hydrogen-Terminated Si(100) Surfaces for Electroless Metal and “Synthetic Metal” Deposition (2004)

Pristine and resist-patterned Si(100) substrates were etched by aqueous HF to produce hydrogen-terminated silicon (H-Si(100)) surfaces. The H-Si(100) surface was then subjected to UV-induced reactive coupling of 4-vinylaniline (VAn) to produce the VAn monolayer-modified silicon (VAn-Si) surface. The VAn-Si surface was first functionalized with a "synthetic metal" by oxidative graft polymerization of aniline with the aniline moieties of the coupled VAn molecules. The composition and topography of the VAn-Si and polyaniline (PAn)-grafted VAn-Si (PAn-VAn-Si) surfaces were characterized by X-ray photoelectron spectroscopy and atomic force microscopy, respectively. The doping-undoping (protonation-deprotonation) and redox-coupling (metal reduction) behavior, as well as the electrical conductivity, of the surface-grafted PAn were found to be similar to those of the aniline homopolymer. The VAn-Si surface was also funtionalized by the electroless plating of copper. Not only did the VAn layer provide chemisorption sites for the palladium catalyst, in the absence of prior sensitization by SnCl2, during the electroless plating process, it also served as an adhesion promotion layer and a low-temperature diffusion barrier for the electrolessly deposited copper. Finally, micropatterning of the grafted PAn and of the electrolessly deposited copper were demonstrated on the resist-patterned VAn-Si surfaces.