gebhart/patrepeval huggingface dataset:
Editorial: Signals to sociality: how microbial communication fashions communities (2016)

The unicellular and liquid-dwelling lifestyles of bacteria have historically dominated microbiological studies, yet most bacteria exist in nature in multifaceted communities that are often associated with living and non-living surfaces. Within these communities, bacteria are exchanging information with other bacteria and other organisms, including eukaryotes, to generate coordinated behaviors. Central to this microbial information exchange is communication between cells. The act of communication exists in many forms and is often considered essential for organized group behaviors between individuals and for the development of multicellular organisms. The collection of reviews presented in the thematic issue ‘Signals to sociality: how microbial communication fashions communities’ (bit.ly/MicrobialCom) addresses several outstanding questions in microbial cell–cell communication. These reviews highlight aspects of cell–cell communication through the lens of microbial linguistics (which signals are communicated and how), microbial ecology and evolution (how communication impacts individuals within communities over time), microbial sociology (‘sociomicrobiology’ (Parsek and Greenberg 2005), how communication impacts group behaviors), and microbial chemistry (what the intrinsic nature of these signaling molecules is).

Our knowledge of microbial cell–cell communication is vast and rapidly expanding. Traditional quorum sensing was the first mode of cell–cell communication to be described (Nealson, Platt and Hastings 1970; Engebrecht, Nealson and Silverman 1983; Kaplan and Greenberg 1987; Bassler et al . 1993) and is generally considered to be the control of gene expression in response to cell-population density through the production of and response to freely diffusible small molecules. A large number of organisms produce and respond to more than one quorum-sensing molecule, enabling many ‘conversations’ to be conducted simultaneously. In this issue, Hawver et al . consider the fascinating question of how Vibrio cholerae , and other bacteria, distinguish between the quorum-sensing molecule(s) they produce and those to which they respond and adjust their behavior accordingly, a behavior that … 

[↵][1]* Corresponding author: Tel: +1 617-496-1637; E-mail: kagibbs{at}mcb.harvard.edu

 [1]: #xref-corresp-1-1
Temperature-Responsive Liquid Chromatography. 2. Effects of Hydrophobic Groups in N-Isopropylacrylamide Copolymer-Modified Silica (1997)

We recently reported the new concept of temperature-responsive liquid chromatography using temperature-responsive poly(N-isopropylacrylamide)-modified surfaces as high-performance liquid chromatography media with aqueous mobile phases. Incorporation of hydrophobic sites is an important factor to improve the efficacy (selectivity and retention) of temperature-responsive chromatography. Toward this goal, we have synthesized semitelechelic copolymers of N-isopropylacrylamide (IPAAm) and butyl methacrylate (BMA) having reactive terminal functional groups using telomerization. The lower critical solution temperatures of the copolymers shift to lower temperatures with increasing hydrophobic BMA content in the poly(IPAAm-co-BMA) relative to that of the IPAAm homopolymer. This temperature-responsive semitelechelic copolymer was grafted to the surface of (aminopropyl)silica through the reaction of activated ester-amine coupling. The polymer-modified silica was used as a column packing material. Separation of a mixture of five steroids having various hydrophobicities was investigated. Retention of steroids on poly(IPAAm-co-BMA)-modified columns is increased with an increase in column temperature. The capacity factors for steroids on the copolymer-modified silica beads was much larger than that on homopolymer PIPAAm-modified columns. The capacity factor for testosterone at 50 degrees C was 33.8 for poly(IPAAm-co-BMA) containing 5 mol% BMA, while that for the PIPAAm homopolymer was 15.0 at the same temperature. The influence of column temperature on steroid retention behavior on copolymer-modified stationary phases was significant compared with the case of homopolymer-modified columns. Furthermore, retention times for steroids increased remarkably with increasing BMA composition. The temperature-responsive elution behavior for the steroids was strongly affected by the hydrophobicity of the grafted polymer chains on silica surfaces. Possible protein separation in temperature-responsive liquid chromatography was explored using insulin chains A and B, and beta-endorphin fragment 1-27. On IBc-3.2-modified silica column, these three peptides were successfully separated at 30 degrees C with 0.5 M NaCl aqueous solution (pH 2.1) as mobile phase. The retention times of these peptides were related to the number of hydrophobic amino acid residues in the peptides. In the proposed chromatography system, elution of target substances is controlled only by a small change in column temperature without any further modification of the aqueous mobile phase.
An IκB‐β COOH terminal region protein is essential for the proliferation of CHO cells under acidic stress (2004)

CHO-K1 cells were able to proliferate and maintain pHi homeostasis at pH 6.3. A novel acidic sensitive mutant, AS-5B, which proliferated at pH 7.4 but failed to either proliferate or maintain pHi homeostasis at pH 6.3, was derived from CHO-K1 using a replica method. The acidic-sensitivity of AS-5B was not due to deficiencies in sodium proton exchangers, HCO3- (co)transporters or H+-ATPases. A cDNA clone encoding a COOH terminal region of IkappaB-beta conferred partial acidic-resistance on AS-5B, and the encoded protein was present in CHO-K1, but was nearly absent from AS-5B. Our data demonstrated that the expression of this small protein was essential for the proliferation of CHO cells under acidic stress.
Motif-Based Hyponym Relation Extraction from Wikipedia Hyperlinks (2014)

Discovering hyponym relations among domain-specific terms is a fundamental task in taxonomy learning and knowledge acquisition. However, the great diversity of various domain corpora and the lack of labeled training sets make this task very challenging for conventional methods that are based on text content. The hyperlink structure of Wikipedia article pages was found to contain recurring network motifs in this study, indicating the probability of a hyperlink being a hyponym hyperlink. Hence, a novel hyponym relation extraction approach based on the network motifs of Wikipedia hyperlinks was proposed. This approach automatically constructs motif-based features from the hyperlink structure of a domain; every hyperlink is mapped to a 13-dimensional feature vector based on the 13 types of three-node motifs. The approach extracts structural information from Wikipedia and heuristically creates a labeled training set. Classification models were determined from the training sets for hyponym relation extraction. Two experiments were conducted to validate our approach based on seven domain-specific datasets obtained from Wikipedia. The first experiment, which utilized manually labeled data, verified the effectiveness of the motif-based features. The second experiment, which utilized an automatically labeled training set of different domains, showed that the proposed approach performs better than the approach based on lexico-syntactic patterns and achieves comparable result to the approach based on textual features. Experimental results show the practicability and fairly good domain scalability of the proposed approach.
Human Lactoferrin Interacts with Soluble CD14 and Inhibits Expression of Endothelial Adhesion Molecules, E-Selectin and ICAM-1, Induced by the CD14-Lipopolysaccharide Complex (2000)

Lipopolysaccharides (LPS), either in the free form or complexed to CD14, a LPS receptor, are elicitors of the immune system. Lactoferrin (Lf), a LPS-chelating glycoprotein, protects animals against septic shock. Since optimal protection requires administration of Lf prior to lethal doses of LPS, we hypothesized that interactions between Lf and soluble CD14 (sCD14) exist. In a first step, human sCD14 and human Lf (hLf) were used to determine the kinetic binding parameters of hLf to free sCD14 in an optical biosensor. The results demonstrated that hLf bound specifically and with a high affinity (K(d) = 16+/-7 nM) to sCD14. Affinity chromatography studies showed that hLf interacted not only with free sCD14 but also, though with different binding properties, with sCD14 complexed to LPS or lipid A-2-keto-3-deoxyoctonic acid-heptose. In a second step, we have investigated whether the capacity of hLf to interact with sCD14 could modulate the expression of endothelial-leukocyte adhesion molecule 1 (E-selectin) or intercellular adhesion molecule 1 (ICAM-1) induced by the sCD14-LPS complex on human umbilical vein endothelial cells (HUVEC). Our experiments show that hLf significantly inhibited both E-selectin and ICAM-1 expressions at the surface of HUVEC. In conclusion, these observations suggest that the anti-inflammatory effects of hLf are due not only to the ability of the molecule to chelate LPS but also to its ability to interact with sCD14 and with the sCD14 complexed to LPS, thus modifying the activation of endothelial cells.
The circulating calcification inhibitors, fetuin-A and osteoprotegerin, but not Matrix Gla protein, are associated with vascular stiffness and calcification in children on dialysis (2008)

This is the first study to define normal levels of the calcification inhibitors in children and show that fetuin-A and OPG are associated with increased vascular stiffness and calcification in children on dialysis. Higher levels of fetuin-A in children suggest a possible protective upregulation of fetuin-A in the early stages of exposure to the pro-calcific and pro-inflammatory uraemic environment.
Broadband LP01/LP11 PLC-based mode multi/demultiplexer designed by wavefront matching method (2015)

A broadband, large fabrication tolerance LP01/LP11 PLC-based mode multi/demultiplexer design is presented by using wavefront mathing method. The low-loss (−0.3 dB) bandwidth of the optimized structure (350 nm) is 4-times wider than that of conventional structure (90 nm).
Voltage-activated calcium channel currents of rat DRG neurons are reduced by mercuric chloride (HgCl2) and methylmercury (CH3HgCl). (1996)

The actions of bath applied mercuric chloride (HgCl2) and methylmercury (CH3HgCl) on voltage-activated calcium channel currents (VACCCs) were tested, using the whole cell patch clamp recording technique with cultured dorsal root ganglion (DRG) neurons from 2-4 day old rat pups. Both metal compounds reduced the current irreversibly in a concentration dependent fashion, reaching a new (lower) steady state within 3 to 5 min after application. Inorganic mercury was more effective in reducing the VACCCs with an IC50 of 1.3 microM, while the IC50 for methylmercury was 2.6 microM. But the threshold concentrations were below 0.25 microM for both metal compounds and the calcium channel currents were reduced by more than 90% with concentrations of 5 microM and 20 microM, respectively. The Hill coefficient for both dose-response relationship was calculated as approximately 1. Calcium channel currents were reduced over the entire voltage range, but the current-voltage relation shifted to more positive potentials in a concentration dependent manner, the effect being more pronounced with HgCl2 than with CH3HgCl (1 microM HgCl2: 10 mV shift, 5 microM CH3HgCl: 5 mV shift). At higher concentrations (> or = 2 microM for HgCl2, and > or = 10 microM for CH3HgCl) an unidentified membrane current was observed. The inorganic mercury caused an inward current, while the organic mercury compound generated a biphasic current with a transient inward and a long lasting outward component. Our results suggest that mercury compounds affect the electrical properties of neurons and thereby decrease cognitive and motor performance.
Macromolecular Proton Fraction as a Myelin Biomarker: Principles, Validation, and Applications (2022)

Macromolecular proton fraction (MPF) is a quantitative MRI parameter describing the magnetization transfer (MT) effect and defined as a relative amount of protons bound to biological macromolecules with restricted molecular motion, which participate in magnetic cross-relaxation with water protons. MPF attracted significant interest during past decade as a biomarker of myelin. The purpose of this mini review is to provide a brief but comprehensive summary of MPF mapping methods, histological validation studies, and MPF applications in neuroscience. Technically, MPF maps can be obtained using a variety of quantitative MT methods. Some of them enable clinically reasonable scan time and resolution. Recent studies demonstrated the feasibility of MPF mapping using standard clinical MRI pulse sequences, thus substantially enhancing the method availability. A number of studies in animal models demonstrated strong correlations between MPF and histological markers of myelin with a minor influence of potential confounders. Histological studies validated the capability of MPF to monitor both demyelination and re-myelination. Clinical applications of MPF have been mainly focused on multiple sclerosis where this method provided new insights into both white and gray matter pathology. Besides, several studies used MPF to investigate myelin role in other neurological and psychiatric conditions. Another promising area of MPF applications is the brain development studies. MPF demonstrated the capabilities to quantitatively characterize the earliest stage of myelination during prenatal brain maturation and protracted myelin development in adolescence. In summary, MPF mapping provides a technically mature and comprehensively validated myelin imaging technology for various preclinical and clinical neuroscience applications.
Leptin and IL-6 Family Cytokines Synergize to Stimulate Müller Glia Reprogramming and Retina Regeneration (2014)

Unlike mammals, zebrafish can regenerate a damaged retina. This remarkable regenerative response is mediated by Müller glia (MG) that undergo a reprogramming event that drives their proliferation and the generation of multipotent progenitors for retinal repair. The mechanisms that drive MG reprogramming are poorly understood. Here, we report that Leptin and Gp130-coupled receptors, acting via a Jak/Stat signaling pathway, stimulate MG reprogramming and progenitor formation in the injured retina. Importantly, we find that ascl1a gene expression, which drives MG reprogramming in fish and mammals, is regulated in a Jak/Stat-dependent manner and requires consensus Stat-binding sites for injury-dependent activation. Finally, we identify cytokines that are induced by retinal injury and exhibit a remarkable synergy in their ability to activate Jak/Stat signaling and MG reprogramming in the uninjured retina. Our study not only furthers our understanding of retina regeneration in zebrafish but also suggests new strategies for awakening retina regeneration in mammals.
High throughput phospholipid fatty acid analysis of soils (2012)

Phospholipid fatty acid (PLFA) analysis is widely used to measure microbial biomass and community composition in soil and other types of environmental samples. As typically performed, the analysis involves many steps and 1.5–3 days are required to prepare a small batch (i.e. 20–24 samples and blanks), depending on the exact equipment employed in each laboratory. Gas chromatography (GC) or gas chromatography–mass spectrometry (GC–MS) is then used to analyze the samples, requiring further time to obtain the data. We have developed a method for preparing 96 soil samples and blanks in 1.5 days, a 4- to 5-fold increase in throughput. All drying and centrifuging steps take place in a centrifugal evaporator. Soil samples in test tubes are dried overnight and then a Bligh–Dyer lipid extraction is performed. The extract is dried, dissolved in chloroform, and loaded onto a 96-well solid phase extraction plate. Phospholipids are eluted into glass vials in a 96-well format, dried, and transesterified. The resulting fatty acid methyl esters are analyzed by GC and quantified relative to an internal standard. The high throughput protocol uses much smaller solvent volumes than the traditional protocol, which combined with the use of the 96-well format leads to much faster sample preparation. Biomarker PLFA concentrations for 10 different soils were highly correlated, although not identical, between the two protocols. Multivariate analysis of the PLFA biomarkers indicated that the two protocols produced similar patterns for the different soils. The high throughput protocol may be useful to laboratories performing large numbers of PLFA analyses.
Exome Sequencing in the Clinical Diagnosis of Sporadic or Familial Cerebellar Ataxia (2014)

This study demonstrated that clinical exome sequencing in patients with adult-onset and sporadic presentations of ataxia is a high-yield test, providing a definitive diagnosis in more than one-fifth of patients and suggesting a potential diagnosis in more than one-third to guide additional phenotyping and diagnostic evaluation. Therefore, clinical exome sequencing is an appropriate consideration in the routine genetic evaluation of all patients presenting with chronic progressive cerebellar ataxia.
Increased dense erythrocytes in flame-burned patients (2013)

We have demonstrated that in vivo dense erythrocytes can be generated in the setting of flame burns. Thus, the underlying reason may be oxidant injury as represented by the reduced level of GSH that we found in association with the generation of dense erythrocytes.
Platform Behavior under Market Shocks: A Simulation Framework and Reinforcement-Learning Based Study (2022)

We study the behavior of an economic platform (e.g., Amazon, Uber Eats, Instacart) under shocks, such as COVID-19 lockdowns, and the effect of different regulation considerations imposed on a platform. To this end, we develop a multi-agent Gym environment of a platform economy in a dynamic, multi-period setting, with the possible occurrence of economic shocks. Buyers and sellers are modeled as economically-motivated agents, choosing whether or not to pay corresponding fees to use the platform. We formulate the platform's problem as a partially observable Markov decision process, and use deep reinforcement learning to model its fee setting and matching behavior. We consider two major types of regulation frameworks: (1) taxation policies and (2) platform fee restrictions, and offer extensive simulated experiments to characterize regulatory tradeoffs under optimal platform responses. Our results show that while many interventions are ineffective with a sophisticated platform actor, we identify a particular kind of regulation -- fixing fees to optimal, pre-shock fees while still allowing a platform to choose how to match buyer demands to sellers -- as promoting the efficiency, seller diversity, and resilience of the overall economic system.
Printing processes and their potential for RFID printing (2005)

This paper explains the basics of a number of printing processes (offset lithography, gravure, flexography, ink jet, electrophotography and screen printing). Characteristics such as the process principles, the type of inks and substrates used, the resolution, but also the limitations of these processes (in terms of regularity, for instance) are tackled. Then, their potential for RFID printing is addressed.
Mitogenic Signalling and Substrate Specificity of the Flk2/Flt3 Receptor Tyrosine Kinase in Fibroblasts and Interleukin 3-Dependent Hematopoietic Cells (1993)

Flk2/Flt3 is a recently identified receptor tyrosine kinase expressed in brain, placenta, testis, and primitive hematopoietic cells. The mitogenic signalling potential and biochemical properties of Flk2/Flt3 have been analyzed by using a chimeric receptor composed of the extracellular domain of the human colony-stimulating factor 1 receptor and the transmembrane and cytoplasmic domains of murine Flk2/Flt3. We demonstrate that colony-stimulating factor 1 stimulation of the Flk2/Flt3 kinase in transfected NIH 3T3 fibroblasts leads to a transformed phenotype and generates a full proliferative response in the absence of other growth factors. In transfected interleukin 3 (IL-3)-dependent Ba/F3 lymphoid cells, activation of the chimeric receptor can abrogate IL-3 requirement and sustain long-term proliferation. We show that phospholipase C-gamma 1, Ras GTPase-activating protein, the p85 subunit of phosphatidylinositol 3'-kinase, Shc, Grb2, Vav, Fyn, and Src are components of the Flk2/Flt3 signal transduction pathway. In addition, we demonstrate that phospholipase C-gamma 1, the p85 subunit of phosphatidylinositol 3'-kinase, Shc, Grb2, and Src family tyrosine kinases, but not Ras GTPase-activating protein, Vav, or Nck, physically associate with the Flk2/Flt3 cytoplasmic domain. Cell-type-specific differences in tyrosine phosphorylation of p85 and Shc are observed. A comparative analysis of the Flk2/Flt3 signal cascade with those of the endogenous platelet-derived growth factor and IL-3 receptors indicates that Flk2/Flt3 displays specific substrate preferences. Furthermore, tyrosine phosphorylation of p85 and Shc is similarly affected by totally different growth factors in the same cellular background.
Efficient and Eco‐Friendly Process for the Synthesis of Bis(1H‐indol‐3‐yl)methanes using Ionic Liquids (2003)

Abstract Indoles react smoothly with carbonyl compounds in 1‐butyl‐3‐methylimidazolium tetrafluoroborate ([bmim]BF 4 ) or 1‐butyl‐3‐methylimidazolium hexafluorophosphate ([bmim]PF 6 ) ionic liquids under mild reaction conditions to afford the corresponding bis‐indolylmethanes in excellent yields. These ionic liquids can be recovered and recycled in subsequent reactions without any apparent loss of activity.
Yeast FIT2 homolog is necessary to maintain cellular proteostasis by regulating lipid homeostasis (2020)

Lipid droplets (LDs) have long been regarded as inert cytoplasmic organelles with the primary function of housing excess intracellular lipids. More recently, LDs have been strongly implicated in conditions of lipid and protein dysregulation. The fat storage inducing transmembrane (FIT) family of proteins comprises of evolutionarily conserved endoplasmic reticulum (ER)-resident proteins that have been reported to induce LD formation. Here, we establish a model system to study the role of S. cerevisiae FIT homologues ( ScFIT ), SCS3 and YFT2 , in proteostasis and stress response pathways. While LD biogenesis and basal ER stress-induced unfolded protein response (UPR) remain unaltered in ScFIT mutants, SCS3 was found to be essential for proper stress-induced UPR activation and for viability in the absence of the sole yeast UPR transducer IRE1. Devoid of a functional UPR, scs3 mutants exhibited accumulation of triacylglycerol within the ER along with aberrant LD morphology, suggesting a UPR-dependent compensatory mechanism for LD maturation. Additionally, SCS3 was necessary to maintain phospholipid homeostasis. Strikingly, the absence of the ScFIT proteins results in the downregulation of the closely-related Heat Shock Response (HSR) pathway. In line with this observation, global protein ubiquitination and the turnover of both ER and cytoplasmic misfolded proteins is impaired in ScFIT cells, while a screen for interacting partners of Scs3 identifies components of the proteostatic machinery as putative targets. Taken together, these suggest that ScFIT proteins may modulate proteostasis and stress response pathways with lipid metabolism at the interface between the two cellular processes.