gebhart/patrepeval huggingface dataset:
Chemistry towards Biology—Instruct: Snapshot (2022)

The knowledge of interactions between different molecules is undoubtedly the driving force of all contemporary biomedical and biological sciences. Chemical biology/biological chemistry has become an important multidisciplinary bridge connecting the perspectives of chemistry and biology to the study of small molecules/peptidomimetics and their interactions in biological systems. Advances in structural biology research, in particular linking atomic structure to molecular properties and cellular context, are essential for the sophisticated design of new medicines that exhibit a high degree of druggability and very importantly, druglikeness. The authors of this contribution are outstanding scientists in the field who provided a brief overview of their work, which is arranged from in silico investigation through the characterization of interactions of compounds with biomolecules to bioactive materials.
Odd–Even Effect in the Hydrophobicity of n-Alkanethiolate Self-Assembled Monolayers Depends upon the Roughness of the Substrate and the Orientation of the Terminal Moiety (2014)

The origin of the odd-even effect in properties of self-assembled monolayers (SAMs) and/or technologies derived from them is poorly understood. We report that hydrophobicity and, hence, surface wetting of SAMs are dominated by the nature of the substrate (surface roughness and identity) and SAM tilt angle, which influences surface dipoles/orientation of the terminal moiety. We measured static contact angles (θs) made by water droplets on n-alkanethiolate SAMs with an odd (SAM(O)) or even (SAM(E)) number of carbons (average θs range of 105.8-112.1°). When SAMs were fabricated on smooth "template-stripped" metal (M(TS)) surfaces [root-mean-square (rms) roughness = 0.36 ± 0.01 nm for Au(TS) and 0.60 ± 0.04 nm for Ag(TS)], the odd-even effect, characterized by a zigzag oscillation in values of θs, was observed. We, however, did not observe the same effect with rougher "as-deposited" (M(AD)) surfaces (rms roughness = 2.27 ± 0.16 nm for Au(AD) and 5.13 ± 0.22 nm for Ag(AD)). The odd-even effect in hydrophobicity inverts when the substrate changes from Au(TS) (higher θs for SAM(E) than SAM(O), with average Δθs |n - (n + 1)| ≈ 3°) to Ag(TS) (higher θs for SAM(O) than SAM(E), with average Δθs |n - (n + 1)| ≈ 2°). A comparison of hydrophobicity across Ag(TS) and Au(TS) showed a statistically significant difference (Student's t test) between SAM(E) (Δθs |Ag evens - Au evens| ≈ 5°; p < 0.01) but failed to show statistically significant differences on SAM(O) (Δθs |Ag odds - Au odds| ≈ 1°; p > 0.1). From these results, we deduce that the roughness of the metal substrate (from comparison of M(AD) versus M(TS)) and orientation of the terminal -CH2CH3 (by comparing SAM(E) and SAM(O) on Au(TS) versus Ag(TS)) play major roles in the hydrophobicity and, by extension, general wetting properties of n-alkanethiolate SAMs.
Related Article from The Quest for Self-Identity: Not All Cancer Stem Cells Are the Same (2023)

Related Article from The Quest for Self-Identity: Not All Cancer Stem Cells Are the Same
The Role of Zinc Layer During Wetting of Aluminium on Zinc-coated Steel in Laser Brazing and Welding (2014)

The zinc layer of zinc-coated steel is known to be a crucial factor for the spreading of liquid aluminium on the coated surface. For industrial brazing and welding processes these zinc-coatings enable a fluxless joining between aluminium and steel in many cases. Yet, the reason for the beneficial effect of the zinc to the wetting process is not completely understood. Fundamental investigations on the wetting behaviour of single aluminium droplets on different zinc-coated steel surfaces have revealed a distinct difference between coated surfaces at room temperature and at elevated temperature regarding the influence of different coating thicknesses. In this paper the case of continuous laser brazing and welding processes of aluminium and commercial galvanized zinc-coated steel sheets are presented. It is shown that in the case of bead-on-plate laser beam brazing, the coating thickness has a measureable effect on the resulting wetting angle and length but does not have a significant impact in case of overlap laser beam welding. This might be linked to different heat transfer conditions. The results also strongly indicate that proper initialbreakup of oxide layers is still required to accomplish good wetting on zinc-coated surfaces.
Sensitivity and specificity of diastolic indexes for rejection surveillance: temporal correlation with endomyocardial biopsy. (1992)

Although acute diastolic dysfunction is an early sequela of the rejecting heart, reported sensitivities and specificities have varied widely when Doppler echocardiography is used for rejection surveillance. This study examines the temporal relationship between changes in Doppler echocardiographic indexes of diastolic function and sequential endomyocardial biopsies to identify possible factors accounting for false-positive and false-negative results. A total of 114 Doppler echocardiographic studies and biopsies were performed weekly in 39 patients aged 14 to 59 years during the initial 3 months after heart transplantation. All Doppler examinations were within 24 hours of biopsy and were analyzed in a blinded fashion. Onset of restrictive physiology, defined as a 15% decrease in either isovolumic relaxation time or pressure half-time, was determined by analysis of the Doppler mitral flow velocity curve.
Establishment of Native Insulin‐Negative NOD Mice and the Methodology to Distinguish Specific Insulin Knockout Genotypes and a B:16 Alanine Preproinsulin Transgene (2004)

We hypothesize that NOD mice without native insulin, but with an altered insulin B:9-23 sequence, will be completely protected from diabetes/insulitis if insulin B:9-23 is an essential T cell epitope. To investigate this hypothesis, we have established initial insulin 1- and 2-negative NOD mice with a transgene directing production of preproinsulin with alanine at position B:16 rather than the native tyrosine of both insulin 1 and insulin 2. Sets of primers for PCR-based assays have been created and validated. They are able to distinguish the presence or absence of the insulin gene knockouts and of both native insulin 1 and insulin 2 (and thus distinguish heterozygous versus homozygous knockouts), as well as the presence of the altered insulin transgene, B:16 alanine preproinsulin. Four B:16 alanine transgenic founders were produced directly in NOD mice and, by intercrossing, initial live native insulin-negative B:16 alanine transgenic mice have been generated.
Chemiluminescence studies. IV. Pressure-dependent photon yields for Ba, Sm, and Eu reactions with N$sub 2$O, O$sub 3$, O$sub 2$, F$sub 2$, and NF$sub 3$ (1975)

Chemiluminescence spectra and photon yields are presented for reactions of Ba, Sm, and Eu with N$sub 2$O, O$sub 3$, O$sub 2$, F2$sub 2$, and NF$sub 3$ for the pressure range 0.5 to 20 torr. Peak yields range from 2.5 percent to 70 percent, with the reactions of Sm with NF$sub 3$ and F$sub 2$ having the highest yields. These latter reactions put from 12 percent to 16 percent of their available thermal energy into luminous output. The pressure dependence of the photon yields deduced from these and other recent measurements suggests that the initial exothermic reaction primarily populates high vibrational levels of the ground electronic state of the newly formed diatomic. Radiating states would then be populated mainly by collision-induced vibrational-to-electronic internal conversion. (auth)
Effect of Pore Structure on the Electrochemical Capacitive Performance of MnO[sub 2] (2007)

Three types of porous : ordered mesoporous , disordered mesoporous , and disordered porous were synthesized using hard template, self-assembly, co-precipitation methods, respectively. The electrochemical capacitance profiles have been evaluated in aqueous solution by means of cyclic voltammetry and impedance measurements. The capacitance profile of the three types of 1D tunnel structure is clearly dependent upon its pore structure despite its crystalline structure. The three porous deliver a capacitance of . Compared to the disordered porous , the ordered mesoporous and disordered mesoporous , especially for the ordered mesoporous , shows better rate capability due to the unique structure of their well ordered mesoporous network, which is more favorable for fast ionic transport than in the disordered porous .
Transducer Adaptive Ultrasound Volume Reconstruction (2021)

Reconstructed 3D ultrasound volume provides more context information than a sequence of 2D scanning frames, which is desirable for various clinical applications such as ultrasound-guided prostate biopsy. Nevertheless, 3D volume reconstruction from freehand 2D scans is very challenging, especially without external tracking devices. Recent deep learning-based methods demonstrate the potential of directly estimating inter-frame motion between consecutive ultrasound frames. However, such algorithms are specific to particular transducers and scanning trajectories associated with the training data, which may not be generalized to other image acquisition settings. In this paper, we formulate the difference in data acquisition as domain shift and propose a novel domain adaptation strategy to adapt deep learning algorithms to data acquired using a different transducer. Specifically, feature extractors generating transducer-invariant features get trained by minimizing the discrepancy between image features of paired samples in a latent space. Our results show that the proposed domain adaptation method can successfully align different feature distributions while preserving the transducer-specific information for universal freehand ultrasound volume reconstruction.
Photoelectrochromic Dithienylperfluorocyclopentene Derivatives (2004)

Abstract Dithienylperfluorocyclopentene derivatives that bear alkyl substituents connected onto the two carbon atoms of the thiophene heterocycles where, in their ring-closed form, the new C–C single bond is formed (the 2-positions of the thiophene), can exhibit photochromic ring-closing, and both photochromic and electrochromic ring-opening.
[Improving maltodextrin specificity by site-saturation engineering of subsite +1 in cyclodextrin glycosyltransferase from Paenibacillus macerans]. (2014)

By engineering the subsite +1 of cyclodextrin glycosyltransferase (CGTase) from Paenibacillus macerans, we improved its maltodextrin specificity for 2-O-D-glucopyranosyl-L-ascorbic acid (AA-2G) synthesis. Specifically, we conducted site-saturation mutagenesis on Leu194, Ala230, and His233 in subsite +1 separately and gained 3 mutants L194N (leucine --> asparagine), A230D (alanine --> aspartic acid), and H233E (histidine --> glutamic acid) produced higher AA-2G yield than the wild-type and the other mutant CGTases. Therefore, the 3 mutants L194N, A230D, and H233E were further used to construct the double and triple mutations. Among the 7 obtained combinational mutants, the triple mutant L194N/A230D/H233E produced the highest AA-2G titer of 1.95 g/L, which was increased by 62.5% compared with that produced by the wild-type CGTase. Then, we modeled the reaction kinetics of all the mutants and found a substrate inhibition by high titer of L-AA for the mutants. The optimal temperature, pH, and reaction time of all the mutants were also determined. The structure modeling indicated that the enhanced maltodextrin specificity may be related with the changes of hydrogen bonding interactions between the side chain of residue at the three positions (194, 230 and 233) and the substrate sugars.
A Molecular Dynamics Study of Ionomer and Water Adsorption at Carbon Support Materials (2010)

Abstract not Available.
Shampoo Science: A Review of the Physiochemical Processes behind the Function of a Shampoo (2022)

Abstract The components of a shampoo are selected specifically to carry out important roles within the formulation. They must be carefully considered as not only do they act to carry out their own function but they also influence the function of the other components through complexation and other physiochemical interactions. This review focuses on the four principal components in a commercial shampoo formulation: surfactant, deposition polymer, structuring polymer, and viscosity modifiers. The most common molecule types used commercially to carry out the specific roles are discussed, with each of their fundamental functions outlined in detail. The mechanisms by which these molecules can perform these roles are reviewed. Further consideration is taken to outline how components could interact with one another to hinder or facilitate processes.
The effect of periodontal therapy on the survival rate and incidence of complications of multirooted teeth with furcation involvement after an observation period of at least 5 years: a systematic review (2009)

Good long-term survival rates (up to 100%) of multirooted teeth with furcation involvement were obtained following various therapeutic approaches. Initial furcation involvement (Degree I) could be successfully managed by non-surgical mechanical debridement. Vertical root fractures and endodontic failures were the most frequent complications observed following resective procedures.
Influence of 3'-azido-2',3'-dideoxyguanosine treatment on amounts of TERT and POT1 in human HL60 cells (2008)

In human cells, TERT (telomerase reverse transcriptase) is involved in the synthesis of telomere DNA, and POT1 (protection of telomeres 1) is believed to be a regulator of telomere length. We have reported that long-term treatment of human HL60 cells with 50 microM 3'-azido-2',3'-dideoxyguanosine (AZddG) caused telomeres to shorten significantly during early passages (up to 40-50 days), but that telomere length was then stabilized at approximately 2 kbp during later passages. Additionally, cell growth rates showed no obvious change during culture in the presence of 50 microM AZddG. Western blot analysis of these cells showed that the amounts of TERT and POT1 expressed were increased significantly and slightly, respectively. Furthermore, telomeric 3' G-overhangs (G-tails) of AZddG-treated cells were lengthened. These findings suggest that HL60 cells may develop resistance to telomere erosion induced by AZddG.
New Appliances (1960)

data received from the same individuals on previous occasions, and, if the comparison indicated the development of a pathological condition, would send out notices asking the persons in question to seek medical help.The same datahandling systems might be used to construct a giant " Index Medicus " which would help the physician to cietermine the pathological cause of any set of symptoms pr'-sented by a patient and to prescribe a cure for it.New Appliances
Multiantibiotic resistance caused by active drug extrusion in Pseudomonas aeruginosa and other gram-negative bacteria. (1997)

All living organisms have been exposed to noxious compounds throughout their long evolutionary history and those surviving have evolved to fabricate devices that detoxicate and extrude these life threatening substances. It is likely, therefore, that all viable organisms, from bacteria to mammals, are equipped with active extrusion machinery. When bacteria are attacked by antibiotics, they use these tactics to combat the drugs and to develop resistance. Drugs extrusion machinery in Gram-negative bacteria is complex, consisting of the inner membrane transporter which acts as an energy-dependent extrusion pump; a binding protein which presumably connect both membranes; and the outer membrane exit channel. The extrusion pump assemblies are often encoded by chromosomal genes and might be expressed by mutation(s) or induced in the presence of drug(s).
Some deoxygenation reactions with low-valent titanium (titanium trichloride/lithium tetrahydroaluminate) (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome deoxygenation reactions with low-valent titanium (titanium trichloride/lithium tetrahydroaluminate)John E. McMurry, Michael G. Silvestri, Michael P. Fleming, Tova Hoz, and Michael W. GraystonCite this: J. Org. Chem. 1978, 43, 17, 3249–3255Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/jo00411a001https://doi.org/10.1021/jo00411a001research-articleACS PublicationsRequest reuse permissionsArticle Views925Altmetric-Citations84LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Resonator surface contamination-a cause of frequency fluctuations? (2003)

The mass loading effects of adsorbing and desorbing contaminant molecules on the magnitude and characteristics of frequency fluctuations are studied in a thickness shear resonator. An equation was derived relating the spectral density of frequency fluctuations to: rates of adsorption and desorption of one species of contaminant molecules; mass per unit area of a monolayer of molecules; frequency constant; thickness of resonator; and number of molecular sites on one resonator surface. The induced phase noises were found to be significant in very high frequency resonators and are not simple functions of the percent area contaminated. The spectral density of frequency fluctuations was inversely proportional to the fourth power of the thickness if other parameters were held constant. Since the resonator frequency is inversely proportional to the thickness, the spectral density is, in effect, proportional to the fourth power of resonator frequency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains (2021)

The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects.
Endothelial mechanotransduction, nitric oxide and vascular inflammation (2006)

Numerous aspects of vascular homeostasis are modulated by nitric oxide and reactive oxygen species (ROS). The production of these is dramatically influenced by mechanical forces imposed on the endothelium and vascular smooth muscle. In this review, we will discuss the effects of mechanical forces on the expression of the endothelial cell nitric oxide synthase, production of ROS and modulation of endothelial cell glutathione. We will also review data that exercise training in vivo has a similar effect as laminar shear on endothelial function and discuss the clinical relevance of these basic findings.
Role of Perfusion-Weighted Imaging in a Diffusion-Weighted-Imaging-Negative Transient Ischemic Attack (2017)

PWI is useful in defining whether or not the transient neurological symptoms in DWI-negative TIA are true vascular events, and will help to improve the understanding of the pathomechanism of TIA.
Role of Charged Residues in the Catalytic Mechanism of Hepatitis C Virus NS3 Protease:  Electrostatic Precollision Guidance and Transition-State Stabilization (2000)

Maturational cleavage of the hepatitis C virus polyprotein involves the viral chymotrypsin-like serine protease NS3. The substrate binding site of this enzyme is unusually flat and featureless. We here show that NS3 has a highly asymmetric charge distribution that is characterized by strong positive potentials in the vicinity of its active site and in the S5/S6 region. Using electrostatic potential calculations, we identified determinants of this positive potential, and the role of six different residues was explored by site-directed mutagenesis. Mutation of residues in the vicinity of the active site led to changes in k(cat) values of a peptide substrate indicating that basic amino acids play a role in the stabilization of the transition state. Charge neutralization in the S5/S6 region increased the K(m) values of peptide substrates in a manner that depended on the presence of negatively charged residues in the P5 and P6 positions. K(i) values of hexapeptide acids spanning P6-P1 (product inhibitors) were affected by charge neutralization in both the active site region and the S5/S6 region. Pre-steady-state kinetic data showed that the electrostatic surface potential is used by this enzyme to enhance collision rates between peptidic ligands and the active site. Calculations of the interaction energies of protease-substrate or protease-inhibitor complexes showed that electrostatic interaction energies oppose the formation of a tightly bound complex due to an unfavorable change in the desolvation energy. We propose that desolvation costs are minimized by avoiding the formation of individual ion pair interactions through the use of clusters of positively charged residues in the generation of local electrostatic potentials.
Snake Venom Toxins (1974)

Abstract A toxin, designated Ta2, has been isolated from the venom of the green mamba, Dendroaspis angusticeps, by ion exchange chromatography on Amberlite CG-50 and gel filtration through Sephadex G-50. Toxin Ta2 contains 60 amino acid residues, is devoid of phenylalanine and tryptophan, and is cross-linked by four intramolecular disulfide bridges. In its primary structure toxin Ta2 reveals homology with both the neuro- and cardiotoxins. Toxin Ta2 differs immunochemically completely from the long and short neurotoxins, cardiotoxins, and also from D. angusticeps toxin Ta1 (toxin FVII).