gebhart/patrepeval huggingface dataset:
Quorum-sensing control of matrix protein production drives fractal wrinkling and interfacial localization of Vibrio cholerae pellicles (2022)

Abstract Bacterial cells at fluid interfaces can self-assemble into collective communities with stunning macroscopic morphologies. Within these soft, living materials, called pellicles, constituent cells gain group-level survival advantages including increased antibiotic resistance. However, the regulatory and structural components that drive pellicle self-patterning are not well defined. Here, using Vibrio cholerae as our model system, we report that two sets of matrix proteins and a key quorum-sensing regulator jointly orchestrate the sequential mechanical instabilities underlying pellicle morphogenesis, culminating in fractal patterning. A pair of matrix proteins, RbmC and Bap1, maintain pellicle localization at the interface and prevent self-peeling. A single matrix protein, RbmA, drives a morphogenesis program marked by a cascade of ever finer wrinkles with fractal scaling in wavelength. Artificial expression of rbmA restores fractal wrinkling to a Δ rbmA mutant and enables precise tuning of fractal dimensions. The quorum-sensing regulatory small RNAs Qrr1-4 first activate matrix synthesis to launch pellicle primary wrinkling and ridge instabilities. Subsequently, via a distinct mechanism, Qrr1-4 suppress fractal wrinkling to promote fine modulation of pellicle morphology. Our results connect cell-cell signaling and architectural components to morphogenic patterning and suggest that manipulation of quorum-sensing regulators or synthetic control of rbmA expression could underpin strategies to engineer soft biomaterial morphologies on demand.
MAPPIN: a method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants (2017)

Nonsynonymous single nucleotide variants (nsSNVs) constitute about 50% of known disease-causing mutations and understanding their functional impact is an area of active research. Existing algorithms predict pathogenicity of nsSNVs; however, they are unable to differentiate heterozygous, dominant disease-causing variants from heterozygous carrier variants that lead to disease only in the homozygous state. Here, we present MAPPIN (Method for Annotating, Predicting Pathogenicity, and mode of Inheritance for Nonsynonymous variants), a prediction method which utilizes a random forest algorithm to distinguish between nsSNVs with dominant, recessive, and benign effects. We apply MAPPIN to a set of Mendelian disease-causing mutations and accurately predict pathogenicity for all mutations. Furthermore, MAPPIN predicts mode of inheritance correctly for 70.3% of nsSNVs. MAPPIN also correctly predicts pathogenicity for 87.3% of mutations from the Deciphering Developmental Disorders Study with a 78.5% accuracy for mode of inheritance. When tested on a larger collection of mutations from the Human Gene Mutation Database, MAPPIN is able to significantly discriminate between mutations in known dominant and recessive genes. Finally, we demonstrate that MAPPIN outperforms CADD and Eigen in predicting disease inheritance modes for all validation datasets. To our knowledge, MAPPIN is the first nsSNV pathogenicity prediction algorithm that provides mode of inheritance predictions, adding another layer of information for variant prioritization.
Identification of Hepatitis C Virus Inhibitors Targeting Different Aspects of Infection Using a Cell-Based Assay (2012)

With 2 to 3% of the worldwide population chronically infected, hepatitis C virus (HCV) infection continues to be a major health care burden. Unfortunately, current interferon-based treatment options are not effective in all patients and are associated with significant side effects. Consequently, there is an ongoing need to identify and develop new anti-HCV therapies. Toward this goal, we previously developed a cell-based HCV infection assay for antiviral compound screening based on a low-multiplicity-of-infection approach that uniquely allows for the identification of antiviral compounds that target cell culture-derived HCV (HCVcc) at any step of the viral infection cycle. Using this assay, here we report the screening of the NCI Diversity Set II library, containing 1,974 synthesized chemical compounds, and the identification of compounds with specific anti-HCV activity. In combination with toxicity counterscreening, we identified 30 hits from the compound library, 13 of which showed reproducible and dose-dependent inhibition of HCV with mean therapeutic indices (50% cytotoxic concentration [CC(50)]/50% effective concentration [EC(50)]) of greater than 6. Using HCV pseudotype and replicon systems of multiple HCV genotypes, as well as infectious HCVcc-based assembly and secretion analysis, we determined that different compounds within this group of candidate inhibitors target different steps of viral infection. The compounds identified not only will serve as biological probes to study and further dissect the biology of viral infection but also should facilitate the development of new anti-HCV therapeutic treatments.
ChemInform Abstract: New Syntheses of Per‐N‐alkyl‐substituted Triaza‐ and Tetraaza‐Crown Compounds Containing an Allyloxymethyl Substituent. (1989)

Abstract The seven new polyaza‐crown compounds (III)‐(VI) are prepared as shown for (III).
Characterization of an antigen-specific suppressive factor derived from a cloned suppressor effector T cell line. (1984)

Abstract A cloned effector-type suppressor T cell line, 3D10, which is known to suppress the antibody response against dinitrophenylated keyhole limpet hemocyanin (KLH), produced a soluble KLH-specific factor (TsF) that can replace the function of parental T cell clones. High activity of TsF was released spontaneously into the culture supernatant when cultured in interleukin 2 (IL 2)-containing medium, requiring no antigenic stimulation. The culture supernatant of 3D10 was also capable of inhibiting the KLH-induced proliferative response of primed T cells in an antigen-specific manner. The direct target of TsF was found to be Lyt-1+2- T cells undergoing an early stage of antigen-specific proliferation. TsF was antigen binding but lacked any other serologic markers such as I-J and immunoglobulin heavy chain-linked allotypic determinants on T cells. No genetic restriction was found in its action on allogeneic T cells. The production of IL 2 in proliferative T cells by antigenic stimulation was not inhibited by TsF. These results indicate that the TsF described here is the legitimate mediator produced by the effector-type suppressor T cell that suppresses the antigen-specific responses of Lyt-1+2- T cells. The m.w. of TsF was approximately 75,000.
Compact 2.5&#x2013;2.7 GHz two element MIMO antenna system for modern USB dongle (2012)

This paper presents design of a compact two element planar MIMO antenna system for a modern USB dongle operating in the 2.5-2.7 GHz frequency band. The proposed MIMO antenna consists of two monopole antenna elements. High isolation between the antenna elements needed to realize the required diversity properties is achieved by using a decoupling technique that utilizes a lumped capacitance introduced between the antenna elements. The designed MIMO antenna has a compact size of 10 mm×20 mm (that is 6 and 12 times lower in a corresponding dimension than the operating wave length), more than 200 MHz bandwidth for return loss S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> and insertion loss S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sub> simultaneously, and exhibits pattern diversity when different antenna elements are excited. The performed analysis of the envelope correlation coefficient (that is equal to 0.06) shows superior MIMO antenna system characteristics. The designed antenna has planar structure with the standard FR4 PCB technology and, therefore, low production cost. Experimental measurements of a fabricated antenna system prove the characteristics obtained from electromagnetic simulation.
Functional Mapping of the N-terminal Regulatory Domain in the Human Raf-1 Protein Kinase (1995)

Raf-1 is a serine/threonine kinase poised at a key relay point in mitogenic signal transduction pathways from the cell surface to the nucleus. Activation of the transforming potential of Raf-1 has been associated with N-terminal truncation and/or fusion to other proteins, suggesting that the Raf-1 N-terminal half harbors a negative regulatory domain. Seven internal deletion mutants that together scan the entire N-terminal half of human Raf-1 protein were generated to map functional regions in this regulatory domain. Effects of the deletion mutations on kinase activity of Raf-1 were evaluated using a baculovirus/insect cell overexpression system and an in vitro kinase assay with the known physiological substrate of Raf-1, mitogen-activated protein kinase kinase. Deletion of amino acids 276-323 in the unique sequence between conserved regions 2 and 3 leads to modest elevation of Raf-1 basal kinase activity, whereas deletion of amino acids 133-180 in conserved region 1 results in diminished kinase activity. Surprisingly, none of the Raf-1 N-terminal deletion mutants, including a truncated version that is transforming in rodent fibroblasts, exhibits greatly increased levels of basal kinase activity. In addition, while activation of Raf-1 kinase by Ras requires sequences in conserved region 1, only the C-terminal half containing the kinase domain of Raf-1 is required for activation by Src. These findings demonstrate that N-terminal deletions in Raf-1 do not necessarily result in constitutively elevated basal kinase activity and that the N-terminal regulatory domain is completely dispensable for Raf-1 activation by Src.
CMYK Halftoning Algorithm Based on Direct Binary Search. (2001)

The signs of metabolic syndrome following chronic excessive macronutrient intake include body weight gain, excess visceral adipose deposition, hyperglycaemia, glucose and insulin intolerances, hypertension, dyslipidaemia, endothelial damage, cardiovascular hypertrophy, inflammation, ventricular contractile dysfunction, fibrosis, and fatty liver disease. Recent studies show increased activity of soluble epoxide hydrolase (sEH) during obesity and metabolic dysfunction. We have tested whether sEH inhibition has therapeutic potential in a rat model of diet-induced metabolic syndrome. In these high-carbohydrate, high-fat-fed rats, chronic oral treatment with trans-4-[4-(3-adamantan-1-ylureido)-cyclohexyloxy]-benzoic acid (t-AUCB), a potent sEH inhibitor, alleviated the signs of metabolic syndrome in vivo including glucose, insulin, and lipid abnormalities, changes in pancreatic structure, increased systolic blood pressure, cardiovascular structural and functional abnormalities, and structural and functional changes in the liver. The present study describes the pharmacological responses to this selective sEH inhibitor in rats with the signs of diet-induced metabolic syndrome.
TMEM184b Promotes Axon Degeneration and Neuromuscular Junction Maintenance (2016)

Our work has identified both neuroprotective and neurodegenerative roles for a previously undescribed protein, TMEM184b. TMEM184b mutation causes delayed axon degeneration following peripheral nerve injury, indicating that it participates in the degeneration process. Simultaneously, TMEM184b mutation causes progressive structural abnormalities at neuromuscular synapses and swellings within sensory terminals, and animals with this mutation display profound weakness. Thus, TMEM184b is necessary for normal peripheral nerve terminal morphology and maintenance. Loss of TMEM184b results in accumulation of autophagosomal structures in vivo, fitting with emerging studies that have linked autophagy disruption and neurological disease. Our work recognizes TMEM184b as a new player in the maintenance of the nervous system.
Weinreb Amides in Carbene Chemistry: A Time-Resolved IR Investigation into a Potential Intramolecular Stabilization Mechanism (2010)

A chloromethylhydroxamiccarbene was generated photochemically in an attempt to form an intramolecularly stabilized carbene. A rapidly formed intermediate at 1645 cm(-1) decayed with an observed rate of 1.99 × 10(6) s(-1). Other intermediates were also observed. These also decayed, albeit much more slowly (k(obs) = 3.47 × 10(3) and 1.98 × 10(4) s(-1)). Multiple intermediates are apparently a function of both the proximal N,O-dimethylhydroxamic ester and multiple conformers of both the carbene and precursor.
Impairment of Collateral Formation in Lipoprotein(a) Transgenic Mice (2002)

Overall, a high serum Lp(a) concentration impaired collateral formation. Although the delay of angiogenesis in high serum Lp(a) might diminish angiogenesis, intramuscular injection of HGF plasmid induced therapeutic angiogenesis in the Lp(a) transgenic ischemic hindlimb mouse model as potential therapy for PAD.
Structural tuning intra- versus inter-molecular proton transfer reaction in the excited state (2012)

A series of 2-pyridyl-pyrazole derivatives 1-4 possessing five-membered ring hydrogen bonding configuration are synthesized, the structural flexibility of which is strategically tuned to be in the order of 1 > 2 > 3 > 4. This system then serves as an ideal chemical model to investigate the correlation between excited-state intramolecular proton transfer (ESIPT) reaction and molecular skeleton motion associated with hydrogen bonds. The resulting luminescence data reveal that the rate of ESIPT decreases upon increasing the structural constraint. At sufficiently low concentration where negligible dimerization is observed, ESIPT takes place in 1 and 2 but is prohibited in 3 and 4, for which high geometry constraint is imposed. The results imply that certain structural bending motions associated with hydrogen bonding angle/distance play a key role in ESIPT. This trend is also well supported by the DFT computational approach, in which the barrier associated with ESIPT is in the order of 1 < 2 < 3 < 4. Upon increasing the concentration in cyclohexane, except for 2, the rest of the title compounds undergo ground-state dimerization, from which the double proton transfer takes place in the excited state, resulting in a relatively blue shifted dimeric tautomer emission (cf. the monomer tautomer emission). The lack of dimerization in 2 is rationalized by substantial energy required to adjust the angle of hydrogen bond via twisting the propylene bridge prior to dimerization.
Cyclization Reaction of N-Substituted Mandelhydrazide with Formaldehyde (1978)

Acid-catalysed cyclisation of N-substituted mandelhydrazides 11 and X with paraformaldehyde gave hexahydro-1,2,4,5-tetrazine derivatives.Furthermore, the acetyl group on the nitrogen rearranged to alcoholic oxygen during the reaction of X to give VI.We have previously reportedL that the secondary amides possessing a hydroxyl or a mercapto group at a-,Bor v-position reacted with various carbonyl compounds in the presence of an acidic catalyst to give cyclisation products, oxazolidine, tetrahydro-1,3-oxazine, hexahydro-1,3-oxazepine, thiazolidine, tetrahydro-1.3-thiazineand hexahydro-1,3-thiazepine derivatives.
Some Applications of Field-Ion Atom-Probe Analysis to Iron and Steels (1973)

Small-scale analyses have been made by the field-ion atom-probe technique on high-purity iron containing 0.05 at.-% carbon, on an Fe-4%Mo-0.2%C steel, and an Fe-5%Mo-0.1%N steel. Analysis of the iron–carbon alloy at 50 K showed the presence of iron only (together with hydrogen as a surface impurity) and background levels for all other elements of less than one part per thousand. Determinations made near a grain boundary in the same. material showed a carbon concentration of 0.4 at.-%, indicating segregation but at a level well below monolayer coverage. Analysis of precipitates in the iron–molybdenum–carbon alloy gave a composition of Mo2C, in agreement with previous investigations. Analysis of precipitates in the iron–molybdenum–nitrogen alloy gave a composition of Mo2N with 10% of the molybdenum replaced by iron. These latter two results indicate that the response of the instrument to the various ions is not significantly biased and that the unexpectedly low number of carbon signals from the grain-boundary analyses is not a detection artefact.
Identification of cathepsin K as a novel marker of adiposity in white adipose tissue (2003)

In obesity, adipocytes undergo dramatic morphological and molecular changes associated with alterations in their gene expression profile. To identify genes differentially modulated in white adipose tissue (WAT) of obese db/db mice compared to wild type (wt) mice, we utilized RNA fingerprinting. Among the 52 candidates that we identified, we focused here on cathepsin K (ctsk), a cysteine protease, prevalently localized in lysosomes and involved in bone extracellular matrix degradation. In db/db mice, WAT ctsk mRNA was elevated 5.9-fold, as were Mitf and TFE3 (2- and 3.3-fold respectively), two transcription factors involved in ctsk induction in osteoclasts. Moreover, the level of WAT ctsk mRNA was increased in other obese models including A(y), fat, and tubby (2.8-, 3.2-, and 4.9-fold respectively) and decreased in mice undergoing weight loss. Despite the ubiquitous distribution of the ctsk transcript, we demonstrated that the obesity related increase is specific to the adipocytes. Further, in vitro experiments proved that the abundance of ctsk transcript increases upon adipose conversion of the established cell line of preadipocytes 3T3-F442A. In addition, ctsk gene expression was examined in adipose tissue of 21 lean and obese male subjects and significant correlations with BMI (r = 0.54, P = 0.012) and plasma leptin levels (r = 0.54, P = 0.015) were found. In conclusion, the WAT of obese db/db mice exhibits a different expression profile from that of the wt mice, and cathepsin K can be considered a novel marker of obesity and a target for the inhibition of adipose mass growth.
Synthesis and Biological Study of 4‐Aminopyrimidine‐5‐carboxaldehyde Oximes as Antiproliferative VEGFR‐2 Inhibitors. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
RECENT ADVANCES IN CLAY-CATALYZED ORGANIC TRANSFORMATIONS (2000)

(2000). RECENT ADVANCES IN CLAY-CATALYZED ORGANIC TRANSFORMATIONS. Organic Preparations and Procedures International: Vol. 32, No. 1, pp. 1-40.
Nonshrinking Heat and Acid-Resistant Hydrothermal Cements for Use in Oil and Gas Wells (1978)

Novel hydrothermal cements have been developed for use in the recovery of energy sources from hot and deep wells ranging in temperatures from 150°F to over 1000°F.
Use of precision-fed cecectomized rooster assay and digestible indispensable amino acid scores to characterize plant- and yeast-concentrated proteins for inclusion in canine and feline diets1,2 (2020)

Increased consumer interest in high-quality and novel protein sources has driven the demand for the inclusion of protein-rich ingredients in companion animal diets. Novel protein concentrates, with protein contents of at least 50%, have been used to satisfy these consumer demands. However, minimal information is available regarding the macronutrient composition and protein quality of these ingredients that is needed for proper formulation of pet foods. Therefore, the objectives of this study were to determine the macronutrient and amino acid compositions, standardized amino acid digestibility according to the precision-fed rooster assay, and protein quality using digestible indispensable amino acid score (DIAAS like) of pea protein (PP), potato protein (POP), faba bean protein (FBP), soy protein concentrate (SPC), and dried yeast (DY). Precision-fed rooster assays were conducted using cecectomized roosters to calculate standardized amino acid digestibility and true metabolizable energy corrected for nitrogen (TMEn). For all five protein concentrates, all essential amino acids were highly digestible (88.0% to 96.3%, dry matter basis) with differences (<i>P</i> < 0.05) in only lysine, methionine, and tryptophan digestibilities. The TMEn values were highest for POP (4.22 kcal/g) and DY (3.61 kcal/g). The DIAAS-like values for adult dogs indicated that methionine was the first-limiting amino acid in all protein concentrates except POP, where the first-limiting amino acid was tryptophan. Using Association of American Feed Control Officials (AAFCO)-recommended values for adult cats, DIAAS-like values for methionine were lowest (<i>P</i> < 0.05) for FBP at 81.5%, with all other amino acids for all protein concentrates over 100%. The National Research Council (NRC)-recommended allowances for adult cats indicated that DIAAS-like methionine values for PP (92.7%) and FBP (73.8%) were significantly lower (<i>P</i> < 0.05) with these being the first-limiting amino acids, with the remaining amino acids above 100% for the other protein concentrates. The protein quality and high essential amino acid digestibility of these protein concentrates indicate that they would be viable protein sources in canine and feline diets. However, additional complementary protein sources should be included to meet the requirements of all essential amino acids.
Investigating the Impact of Sample Preparation on Mass Spectrometry-Based Drug-To-Antibody Ratio Determination for Cysteine- and Lysine-Linked Antibody–Drug Conjugates (2020)

Antibody-drug conjugates (ADCs) are heterogeneous biotherapeutics and differ vastly in their physicochemical properties depending on their design. The number of small drug molecules covalently attached to each antibody molecule is commonly referred to as the drug-to-antibody ratio (DAR). Established analytical protocols for mass spectrometry (MS)-investigation of antibodies and ADCs often require sample treatment such as desalting or interchain disulfide bond reduction prior to analysis. Herein, the impact of the desalting and reduction steps-as well as the sample concentration and elapsed time between synthesis and analysis of DAR-values (as acquired by reversed phase liquid chromatography MS (RPLC-MS))-was investigated. It was found that the apparent DAR-values could fluctuate by up to 0.6 DAR units due to changes in the sample preparation workflow. For methods involving disulfide reduction by means of dithiothreitol (DTT), an acidic quench is recommended in order to increase DAR reliability. Furthermore, the addition of a desalting step was shown to benefit the ionization efficiencies in RPLC-MS. Finally, in the case of delayed analyses, samples can be stored at four degrees Celsius for up to one week but are better stored at -20 °C for longer periods of time. In conclusion, the results demonstrate that commonly used sample preparation procedures and storage conditions themselves may impact MS-derived DAR-values, which should be taken into account when evaluating analytical procedures.
Spectral mitosis of the Stokes tone generated by two-tone pumped stimulated Brillouin scattering using a completely spectrally resolved model (2022)

For the first time, a completely spectrally resolved model is used to study SBS for nontrivial spectra. A deeper understanding of Brillouin gain and new physics are revealed, including Stokes tone shifting, broadening, and splitting.