gebhart/patrepeval huggingface dataset:
Human milk glycobiome and its impact on the infant gastrointestinal microbiota (2010)

Human milk contains an unexpected abundance and diversity of complex oligosaccharides apparently indigestible by the developing infant and instead targeted to its cognate gastrointestinal microbiota. Recent advances in mass spectrometry-based tools have provided a view of the oligosaccharide structures produced in milk across stages of lactation and among human mothers. One postulated function for these oligosaccharides is to enrich a specific "healthy" microbiota containing bifidobacteria, a genus commonly observed in the feces of breast-fed infants. Isolated culture studies indeed show selective growth of infant-borne bifidobacteria on milk oligosaccharides or core components therein. Parallel glycoprofiling documented that numerous Bifidobacterium longum subsp. infantis strains preferentially consume small mass oligosaccharides that are abundant early in the lactation cycle. Genome sequencing of numerous B. longum subsp. infantis strains shows a bias toward genes required to use mammalian-derived carbohydrates by comparison with adult-borne bifidobacteria. This intriguing strategy of mammalian lactation to selectively nourish genetically compatible bacteria in infants with a complex array of free oligosaccharides serves as a model of how to influence the human supraorganismal system, which includes the gastrointestinal microbiota.
TNF Deficiency Fails to Protect BAFF Transgenic Mice against Autoimmunity and Reveals a Predisposition to B Cell Lymphoma (2004)

TNF is well characterized as a mediator of inflammatory responses. TNF also facilitates organization of secondary lymphoid organs, particularly B cell follicles and germinal centers, a hallmark of T-dependent Ab responses. TNF also mediates defense against tumors. We examined the role of TNF in the development of inflammatory autoimmune disorders resembling systemic lupus erythematosus and Sjögren's syndrome induced by excess B cell-activating factor belonging to the TNF family (BAFF), by generating BAFF-transgenic (Tg) mice lacking TNF. TNF(-/-) BAFF-Tg mice resembled TNF(-/-) mice, in that they lacked B cell follicles, follicular dendritic cells, and germinal centers, and have impaired responses to T-dependent Ags. Nevertheless, TNF(-/-) BAFF-Tg mice developed autoimmune disorders similar to that of BAFF-Tg mice. Disease in TNF(-/-) BAFF-Tg mice correlates with the expansion of transitional type 2 and marginal zone B cell populations and enhanced T-independent immune responses. TNF deficiency in BAFF-Tg mice also led to a surprisingly high incidence of B cell lymphomas (>35%), which most likely resulted from the combined effects of BAFF promotion of neoplastic B cell survival, coupled with lack of protective antitumor defense by TNF. Thus, TNF appears to be dispensable for BAFF-mediated autoimmune disorders and may, in fact, counter any proneoplastic effects of high levels of BAFF in diseases such as Sjögren's syndrome, systemic lupus erythematosus, and rheumatoid arthritis.
Reagent for Evaluating Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS) Performance in Bottom-Up Proteomic Experiments (2015)

We present a novel proteomic standard for assessing liquid chromatography-tandem mass spectrometry (LC-MS/MS) instrument performance, in terms of chromatographic reproducibility and dynamic range within a single LC-MS/MS injection. The peptide mixture standard consists of six peptides that were specifically synthesized to cover a wide range of hydrophobicities (grand average hydropathy (GRAVY) scores of -0.6 to 1.9). A combination of stable isotope labeled amino acids ((13)C and (15)N) were inserted to create five isotopologues. By combining these isotopologues at different ratios, they span four orders of magnitude within each distinct peptide sequence. Each peptide, from lightest to heaviest, increases in abundance by a factor of 10. We evaluate several metrics on our quadrupole orbitrap instrument using the 6 × 5 LC-MS/MS reference mixture spiked into a complex lysate background as a function of dynamic range, including mass measurement accuracy (MMA) and the linear range of quantitation of MS1 and parallel reaction monitoring experiments. Detection and linearity of the instrument routinely spanned three orders of magnitude across the gradient (500 fmol to 0.5 fmol on column) and no systematic trend was observed for MMA of targeted peptides as a function of abundance by analysis of variance analysis (p = 0.17). Detection and linearity of the fifth isotopologue (i.e., 0.05 fmol on column) was dependent on the peptide and instrument scan type (MS1 vs PRM). We foresee that this standard will serve as a powerful method to conduct both intra-instrument performance monitoring/evaluation, technology development, and inter-instrument comparisons.
Prediction of Core Body Temperature from Multiple Variables (2015)

This paper aims to improve the prediction of rectal temperature (T re) from insulated skin temperature (T is) and micro-climate temperature (T mc) previously reported (Richmond et al., Insulated skin temperature as a measure of core body temperature for individuals wearing CBRN protective clothing. Physiol Meas 2013; 34:1531-43.) using additional physiological and/or environmental variables, under several clothing and climatic conditions. Twelve male (25.8±5.1 years; 73.6±11.5kg; 178±6cm) and nine female (24.2±5.1 years; 62.4±11.5kg; 169±3cm) volunteers completed six trials, each consisting of two 40-min periods of treadmill walking separated by a 20-min rest, wearing permeable or impermeable clothing, under neutral (25°C, 50%), moderate (35°C, 35%), and hot (40°C, 25%) conditions, with and without solar radiation (600W m(-2)). Participants were measured for heart rate (HR) (Polar, Finland), skin temperature (T s) at 11 sites, T is (Grant, Cambridge, UK), and breathing rate (f) (Hidalgo, Cambridge, UK). T mc and relative humidity were measured within the clothing. T re was monitored as the 'gold standard' measure of T c for industrial or military applications using a 10cm flexible probe (Grant, Cambridge, UK). A stepwise multiple regression analysis was run to determine which of 30 variables (T is, T s at 11 sites, HR, f, T mc, temperature, and humidity inside the clothing front and back, body mass, age, body fat, sex, clothing, Thermal comfort, sensation and perception, and sweat rate) were the strongest on which to base the model. Using a bootstrap methodology to develop the equation, the best model in terms of practicality and validity included T is, T mc, HR, and 'work' (0 = rest; 1 = exercise), predicting T re with a standard error of the estimate of 0.27°C and adjusted r (2) of 0.86. The sensitivity and specificity for predicting individuals who reached 39°C was 97 and 85%, respectively. Insulated skin temperature was the most important individual parameter for the prediction of T re. This paper provides novel information about the viability of predicting T c under a wide range of conditions, using predictors which can practically be measured in a field environment.
Domain Organization of the 39-kDa Receptor-associated Protein (1999)

The 39-kDa receptor-associated protein (RAP) is an endoplasmic reticulum resident protein that binds to the low density lipoprotein receptor-related protein (LRP) as well as certain members of the low density lipoprotein receptor superfamily and antagonizes ligand binding. In order to identify important functional regions of RAP, studies were performed to define the domain organization and domain boundaries of this molecule. Differential scanning calorimetry (DSC) experiments revealed that the process of thermal denaturation of RAP is highly reversible and occurs in a broad temperature range with two well resolved heat absorption peaks. A good fit of the endotherm was obtained with four two-state transitions suggesting these many cooperative domains in the molecule. A number of recombinant fragments of RAP were expressed in bacteria, and their domain composition and stability were characterized by DSC, circular dichroism, and fluorescence spectroscopy. The results confirmed that RAP is composed of four independently folded domains, D1, D2, D3, and D4, that encompass residues 1-92, 93-163, 164-216, and 217-323, respectively. The first and the fourth domains preserved their structure and stability when isolated, whereas the compact structure of the fragment corresponding to D2 seems to be altered when isolated from the parent molecule. Isolated D3 was partially degraded during isolation from bacterial lysates. The isolated D4 was capable of binding with high affinity to LRP whereas neither D1 nor D2 bound. At the same time a fragment containing both D1 and D2 exhibited high affinity binding to LRP. These facts combined with the thermodynamic analysis of the melting process of the fragments containing D1 and D2 indicate that these two domains interact with each other and that the proper folding of the second domain into a native-like active conformation requires presence of the first domain.
Perception of taste and smell in elderly persons (1993)

By the turn of the century, there will be considerable shifts in demographics, including a massive increase in our aging population. As we plan for better nutrition in the twenty-first century, the special sensory and nutritional needs of the elderly must be taken into account. Chemosensory losses, specifically decrements in the senses of taste and smell, can lead to inadequate intake, especially in the elderly sick. These losses result not only from anatomic changes that occur during normal aging but also from certain diseases, pharmacological and surgical interventions, radiation, and environmental pollutants. The design of foods for the elderly that could both compensate for these chemosensory losses and meet nutritional needs presents new challenges and opportunities for the food industry.
2-Alkenyl and 2-Alkyl Derivatives of Adenosine and Adenosine-5‘-N-Ethyluronamide:  Different Affinity and Selectivity of E- and Z-Diastereomers at A2A Adenosine Receptors (1996)

A series of new 2-(ar)alkenyl, both Z- and E-diastereomers, and 2-alkyl derivatives of adenosine-5'-N-ethyluronamide (NECA) and adenosine were synthesized and evaluated for their interaction with the A1 and A2A adeosine receptors, to better understand the conformational requirements of the receptor area interacting with the substituents in the 2- and 5'-positions. Partial reduction of the triple bond in 2-alkynyl derivatives of NECA led to compounds whose activity at the A2A receptor subtype was related to Z-E-isomerism, the E-diastereomers being more potent and selective than the Z-ones. Saturation of the side chain markedly reduced compound affinity at adenosine receptors. Specifically, compounds bearing an (E)-alkenyl chain, while maintaining the same affinity at A2A receptors as the corresponding alknyl derivatives, showed an increase in A2A vs A1 selectivity. Hence, the new nucleosides (E)-2-hexenylNECA (12a) and (E)-2-(phenylpentenyl)NECA (12b) exhibited both high A2A receptor affinity (Ki = 1.6 and 3.5 nM, respectively) and A2A vs A1 selectivity (157- and 290-fold, respectively). Moreover, 12a displayed potent antiaggregatory activity, similar to that of the reference compound NECA. Comparison between NECA and adenosine derivatives further demonstrated that the 5'-ethylcarboxamido group is critical for the A2A affinity. These studies indicated that the orientation of the substituent in the 2-position and the nature of the 5'-group in adenosine derivatives are critical to achieve high affinity and selectivity at the A2A adenosine receptor subtype.
lag-1, a gene required for lin-12 and glp-1 signaling in Caenorhabditis elegans, is homologous to human CBF1 and Drosophila Su(H) (1996)

The homologous receptors LIN-12 and GLP-1 mediate diverse cell-signaling events during development of the nematode Caenorhabditis elegans. These two receptors appear to be functionally interchangeable and have sequence similarity to Drosophila Notch. Here we focus on a molecular analysis of the lag-1 gene (lin-12 -and glp-1), which plays a central role in LIN-12 and GLP-1-mediated signal transduction. We find that the predicted LAG-1 protein is homologous to two DNA-binding proteins: human C Promoter Binding Factor (CBF1) and Drosophila Suppressor of Hairless (Su(H)). Furthermore, we show that LAG-1 binds specifically to the DNA sequence RTGGGAA, previously identified as a CBF-1/Su(H)-binding site. Finally, we report that the 5' flanking regions and first introns of the lin-12, glp-1 and lag-1 genes are enriched for potential LAG-1-binding sites. We propose that LAG-1 is a transcriptional regulator that serves as a primary link between the LIN-12 and GLP-1 receptors and downstream target genes in C. elegans. In addition, we propose that LAG-1 may be a key component of a positive feedback loop that amplifies activity of the LIN-12/GLP-1 pathway.
Porcine pulmonary surfactant preparations contain the antibacterial peptide prophenin and a C‐terminal 18‐residue fragment thereof (1999)

Surfactant preparations obtained from porcine lungs by extraction with chloroform/methanol followed by chromatography over Lipidex-5000 are used for treatment of respiratory distress syndrome in preterm infants. These preparations contain about 98% phospholipids and 1-2% of the hydrophobic pulmonary surfactant-associated proteins B and C (SP-B and SP-C). Separation of the proteins in the surfactant preparation by reversed-phase high performance liquid chromatography revealed, in addition to SP-B and SP-C, the presence of three peptides derived from the cathelicidin family of antibacterial peptides. The 79-residue proline-rich peptide prophenin (identical to that isolated from leukocytes), an 80-residue prophenin with an N-terminal pyroglutamic acid residue, and a C-terminal 18-residue fragment of prophenin were found in approximate molar ratios of 1:20:5. A synthetic version of the C-terminal 18-residue peptide exhibits salt-dependent antibacterial activity (higher activity in the absence of salt) against the Gram-positive bacterium Bacillus megaterium Bm11 and, to a lesser extent, against Gram-negative Escherichia coli D21 cells. It appears possible that the presence of prophenin peptides may contribute to the antibacterial properties of surfactant preparations.
Direct Laser Sintering of Metals (2018)

The use of a directed laser bealn source to selectively sinter multiple layers of&#13;\nbinderless metal powder for the purposes of rapid prototyping is described. The&#13;\nwork in this paper is restricted to -325 mesh iron powder, which was sintered&#13;\nusing a C\\V 50 W Nd:YAG laser to approximately 3.5% density. A subsequent&#13;\npost-treatlnent was perfornled to achieve a fully dense saulple. It is envisioned&#13;\nthat such a system can be used to manufacture functional metallic prototypes&#13;\ndirectly from CAD without part-specific tooling.
Design, Synthesis, Structure, and Gas (N 2 , Ar, CO 2 , CH 4 , and H 2 ) Sorption Properties of Porous Metal-Organic Tetrahedral and Heterocuboidal Polyhedra (2005)

A strategy based on assembling metal ions and organic carboxylate links has been applied for the design and synthesis of a new class of porous, truncated tetrahedral and heterocuboidal polyhedra, whose pore size and functionality can be systematically varied. The synthesis of this series of metal-organic polyhedra (MOPs) employs sulfate-capped oxygen-centered iron-carboxylate trimers, Fe3O(CO2)3(-)(SO4)3, as rigid nodes separated by linear (phenyl, biphenyl, terphenyl, and tetrahydropyrene) or trigonal (benzenetriphenyl) links to yield five highly crystalline polyhedra of general formula [NH2(CH3)2]8[Fe12O4(-)(SO4)12(link)x(py)12].G (x = 6 for linear or 4 for trigonal, py = pyridine, G = guests). In this series, the size of each polyhedron has been varied from 20.0 to 28.5 A (on edge), and the corresponding pore diameter from 7.3 to 13.3 A. Gas sorption isotherms were measured for three members of this series to reveal significant uptake of gases (N2, Ar, CO2, H2, CH4) and benzene and exhibit Type I sorption behavior that is indicative of permanent porosity. The apparent surface areas for these compounds range from 387 to 480 m(2)/g.
Heritable endogenous gene regulation in plants with designed polydactyl zinc finger transcription factors (2002)

Zinc finger transcription factors (TFs(ZF)) were designed and applied to transgene and endogenous gene regulation in stably transformed plants. The target of the TFs(ZF) is the Arabidopsis gene APETALA3 (AP3), which encodes a transcription factor that determines floral organ identity. A zinc finger protein (ZFP) was designed to specifically bind to a region upstream of AP3. AP3 transcription was induced by transformation of leaf protoplasts with a transformation vector that expressed a TF(ZF) consisting of the ZFP fused to the tetrameric repeat of herpes simplex VP16's minimal activation domain. Histochemical staining of beta-glucuronidase (GUS) activity in transgenic AP3GUS reporter plants expressing GUS under control of the AP3 promoter was increased dramatically in petals when the AP3-specific TF(ZF) activator was cointroduced. TF(ZF)-amplified GUS expression signals were also evident in sepal tissues of these double-transgenic plants. Floral phenotype changes indicative of endogenous AP3 factor coactivation were also observed. The same AP3-specific ZFP(AP3) was also fused to a human transcriptional repression domain, the mSIN3 interaction domain, and introduced into either AP3GUS-expressing plants or wild-type Arabidopsis plants. Dramatic repression of endogenous AP3 expression in floral tissue resulted when a constitutive promoter was used to drive the expression of this TF(ZF). These plants were also sterile. When a floral tissue-specific promoter from APETALA1 (AP1) gene was used, floral phenotype changes were also observed, but in contrast the plants were fertile. Our results demonstrate that artificial transcriptional factors based on synthetic zinc finger proteins are capable of stable and specific regulation of endogenous genes through multiple generations in multicellular organisms.
Amphiphilic Polymer Brushes Grown from the Silicon Surface by Atom Transfer Radical Polymerization (2001)

Homopolymer and block amphiphilic polymer brushes on silicon wafers have been successfully prepared by combining the self-assembled monolayer of initiator and atom transfer radical polymerization (ATRP). Two methods for self-assembly of initiator monolayer were compared: One was to treat the silicon surface with 6-((2-bromo-2-methyl)propionyloxy)hexyltrichlorosilane solution (solution method), and the other was to treat it with the vapor of 3-aminopropyl)triethoxysilane, followed by amidization with 2-bromoisobutyric acid (vapor method). While the solution method produced particles due to cross-linked products of the chlorosilane on silicon surface, the vapor method gave a uniform surface. The homopolymer brushes of poly(methyl methacrylate) (PMMA) and poly(acrylamide) (PAAM) were prepared by ATRP on the modified silicon wafer by the initiator. The amphiphilic block copolymer brushes consisting of PAAM and PMMA blocks were obtained by using the homopolymer brush as the macroinitiator for the second ATRP polymerization of another monomer. XPS revealed that the first polymer layer of the surface was partly covered with the second polymer layer after block copolymerized with the second monomer. AFM measurement of the amphiphilic block polymer brush imaged different morphology when they were treated with water and toluene. The amphiphilic polymer brush was stretched out from the surface and the individual polymer chains have sufficient free volume to permit the conformational change in different solvents.
Recognition-Based Segmentation Algorithm for On-Line Arabic Handwriting (2009)

In this paper, we introduce an on-line Arabic handwritten recognition system based on new stroke segmentation algorithm. The proposed algorithm uses an over segmentation method that has the advantage of giving all correct segments at least. It is based on arbitrary segmentation followed by segmentation enhancement, consecutive joints connection and finally segmentation point locating. The proposed system gives an excellent recognition rate up to 97% and 92% for words and letter recognition.
Identification of new apolipoprotein B epitopes and haplotypes and their distribution in swine populations (1994)

Results from comparative immunogenetic studies on inheritance and identification of four new apolipoprotein B (apoB) allotypes and three additional apoB haplotypes and their distribution in miniature and domestic swine are presented. Immunological surveys on the four new and 16 previously described Lpb allotypes and genetic analysis of their segregation in progenies, of miniature and domestic swine and their crosses, indicate that three new allotypes designated Lpb9, Lpb10 and Lpb101 are individual (mutant) apoB epitopes, each representing a discriminating marker for one of the new apoB haplotypes specified by three new apoB alleles designated Lpb9, Lpb10 and Lpb101. The fourth allotype, Lpb20, is one of the common epitopes forming the alternative epitope pair with Lpb10, and is a constituent of each of the eight previously described and two new apoB haplotypes. The new apoB alleles have so far been found only in miniature swine, with Lpb10 being the most frequent in the Göttingen, Vietnamese Pot-belly and Japanese Miniature, Lpb9 was detected only in Minnesota Miniature and Lpb101 only in Vietnamese Potbelly. The common allotype, Lpb20, shares immunological similarities with human apoB indicating its ancestral origin, whereas none of the alloreagents detecting the three individual apoB variants, Lpb9, Lpb10 or Lpb101, showed cross-reactivity with human apoB, suggesting their exclusive swine origin and evolvement during speciation through mutations.
Angiotensin II participates in mononuclear cell recruitment in experimental immune complex nephritis through nuclear factor-kappa B activation and monocyte chemoattractant protein-1 synthesis. (1998)

Angiotensin-converting enzyme (ACE) inhibitors reduce macrophage infiltration in several models of renal injury. We approached the hypothesis that angiotensin II (AngII) could be involved in inflammatory cell recruitment during renal damage through the synthesis of monocyte chemoattractant protein-1 (MCP-1). In a model of immune complex nephritis, we observed an up-regulation of renal MCP-1 (mRNA and protein) coincidentally with mononuclear cell infiltration that were markedly reduced by treatment with the ACE inhibitor quinapril. Exposure of cultured rat mesangial cells to AngII increased MCP-1 mRNA expression (2.7-fold) and synthesis (3-fold), similar to that observed with TNF-alpha. Since NF-kappaB is involved in the regulation of MCP-1 gene, we explored whether the effects of AngII were mediated through NF-kappaB activation. Untreated nephritic rats showed increased renal NF-kappaB activity (3.5-fold) that decreased in response to ACE inhibition. In mesangial cells, AngII activated NF-kappaB (4.3-fold), and the NF-kappaB inhibitor pyrrolidine dithiocarbamate abolished the AngII-induced NF-kappaB activation and MCP-1 gene expression. Our results suggest that AngII could participate in the recruitment of mononuclear cells through NF-kappaB activation and MCP-1 expression by renal cells. This could be a novel mechanism that might further explain the beneficial effects of ACE inhibitors in progressive renal diseases.