gebhart/patrepeval huggingface dataset:
Molecular cloning of amphiglycan, a novel integral membrane heparan sulfate proteoglycan expressed by epithelial and fibroblastic cells. (1992)

We have synthesized an antisense oligonucleotide primer that matches a supposedly conserved sequence in messages for heparan sulfate proteoglycans with transmembrane orientations. With the aid of this primer we have amplified partial and selected full-length copies of a message from human lung fibroblasts that codes for a novel integral membrane heparan sulfate proteoglycan. The encoded protein is 198 amino-acids long, with discrete cytoplasmic, transmembrane, and amino-terminal extracellular domains. Except for the sequences that represent putative heparan sulfate chain attachment sites, the extracellular domain of this protein has a unique structure. The transmembrane and cytoplasmic domains, in contrast, are highly similar to the corresponding domains of fibroglycan and syndecan, the two cell surface proteoglycans that figured as models for the design of the antisense primer. This similarity includes the conservation of four tyrosine residues, one immediately in front of the stop transfer sequence and three in the cytoplasmic segment, and of the most proximal and most distal cytoplasmic sequences. The cDNA detects a single 2.6-kb message in cultured human lung fibroblasts and in a variety of human epithelial and fibroblastic cell lines. Polyclonal and monoclonal antibodies raised against the encoded peptide after expression as a beta-galactosidase fusion protein react with the 35-kD coreprotein of a cell surface heparan sulfate proteoglycan of human lung fibroblasts and decorate the surface of many cell types. We propose to name this proteoglycan "amphiglycan" (from the Greek words amphi, "around, on both sides of" and amphoo, "both") referring to its domain structure which extends on both sides of the plasmamembrane, and to its localization around cells of both epithelial and fibroblastic origin.
Isolation of an active heavy-chain variable domain from a homogeneous rabbit antibody by cathepsin B digestion of the aminoethylated heavy chain (1980)

Cathepsin B from bovine liver has been used to cleave the heavy chain of partially reduced and aminoethylated rabbit allotype a1 IgG. Three major cleavages have been identified, one of which appears to be at the peptide bond carboxy terminal to the two adjacent (aminoethyl)cysteine residues at positions 133 and 134. The variable domain of the heavy chain (VH) was isolated by gel filtration from both pooled heterogeneous rabbit IgG and a homogenous rabbit antitype III pneumococcal polysaccharide antibody. This VH inhibited the binding of 125I-labeled (allotype a) IgG to anti-a1 allotypic antibodies. The recombinant molecule consisting of VH and light chain from the homogeneous antibody is active in an antigen binding assay.
Linear and Nonlinear Optical Properties of Cationic Bipyridyl Iridium(III) Complexes: Tunable and Photoswitchable? (2011)

A series of cationic Ir(III) substituted bipyridyl ()(N(∧)N (N(∧)N-bpy) complexes incorporating electron-donor and -acceptor substituents, [Ir(C(∧)N-ppy-R')(2)(N(∧)N-bpy-CH═CH-C(6)H(4)-R)][X] (X(-) = PF(6)(-) or C(12)H(25)SO(3)(-)), 2 (a, R = NEt(2) and R' = Me; b, R = O-Oct and R' = Me; c, R = NO(2) and R' = C(6)H(13); C(∧)N-ppy = cyclometalated 2-phenylpyridine, [Ir(C(∧)N-ppy-Me)(2)(N(∧)N-bpy-CH═CH-thienyl-Me)][PF(6)], 2d, and the dithienylethene (DTE)-containing complex 2e have been synthesized and characterized, and their absorption, luminescence, and quadratic nonlinear optical (NLO) properties are reported. Density functional theory (DFT) and time-dependent-DFT (TD-DFT) calculations on the complexes facilitate a detailed assignment of the excited states involved in the absorption and emission processes. All five complexes are luminescent in a rigid glass at 77 K, displaying vibronically structured spectra with long lifetimes (14-90 μs), attributed to triplet states localized on the styryl-appended bipyridines. The second-order NLO properties of 2a-d and related complexes 1a-d with 1,10-phenanthrolines have been investigated by both electric field induced second harmonic generation (EFISH) and harmonic light scattering (HLS) techniques. They are characterized by high negative EFISH μβ values which decrease when the ion pair strength between the cation and the counterion (PF(6)(-), C(12)H(25)SO(3)(-)) increases. The EFISH response is mainly controlled by metal-to-ligand charge-transfer/ligand-to-ligand charge-transfer (MLCT/L'LCT) processes. A combination of HLS and EFISH techniques is used to evaluate both the dipolar and octupolar contributions to the total quadratic hyperpolarizability, demonstrating that the major contribution is controlled by the octupolar part. The incorporation of a photochromic DTE unit into the N(∧)N-bpy ligand (complex 2e) allows the luminescence to be switched ON or OFF. The photocyclisation of the DTE unit can be triggered by using either UV (365 nm) or visible light (430 nm), leading to an efficient quenching of the ligand-based 77 K luminescence, which can be restored upon irradiation of the closed form at 715 nm. In contrast, no significant modification of the EFISH μβ value is observed upon photocyclization, suggesting that the quadratic NLO response is dominated by the MLCT/L'LCT processes, rather than by the intraligand excited states localized on the substituted bipyridine ligand.
Experimental and model investigation of the time-dependent 2-dimensional distribution of binding in a herringbone microchannel (2008)

A microfluidic device known to mix bulk solutions, the herringbone microchannel, was incorporated into a surface-binding assay to determine if the recirculation of solution altered the binding of a model protein (streptavidin) to the surface. Streptavidin solutions were pumped over surfaces functionalized with its ligand, biotin, and the binding of streptavidin to those surfaces was monitored using surface plasmon resonance imaging. Surface binding was compared between a straight microchannel and herringbone microchannels in which the chevrons were oriented with and against the flow direction. A 3-dimensional finite-element model of the surface binding reaction was developed for each of the geometries and showed strong qualitative agreement with the experimental results. Experimental and model results indicated that the forward and reverse herringbone microchannels substantially altered the distribution of protein binding (2-dimensional binding profile) as a function of time when compared to a straight microchannel. Over short distances (less than 1.5 mm) down the length of the microchannel, the model predicted no additional protein binding in the herringbone microchannel compared to the straight microchannel, consistent with previous findings in the literature.
Use of Antibiotics and Risk of Cancer (2004)

To the Editor: Dr Velicer and colleagues reported an association between use of antibiotics and increased risk of breast cancer. We have several concerns about the design of this study. First, because the authors did not obtain data about other prescription medications, they could not establish that the effect was specifically due to antibiotics. Second, although the regression analyses were adjusted for age and duration of insurance enrollment, the authors apparently did not adjust for other documented confounders, such as body mass index, family history of breast cancer, and age at menarche. Third, other confounding factors that might be correlated with both the need for antibiotics and the risk of breast cancer were not analyzed (eg, smoke exposure, weight fluctuations, and use of ethanol). Finally, the results are inconsistent with data from animal studies that show no relationship between extended antibiotic exposure and breast cancer. Until these issues are addressed we believe that the judicious use of antibiotics is still safe in appropriate patients regardless of the patient’s individual risk of breast cancer.
Long‐term amelioration of rat adjuvant arthritis following systemic elimination of macrophages by clodronate‐containing liposomes (1995)

Clodronate-laden liposomes induce long-term amelioration of AA, even if administered for a brief period during the florid phase of the disease. The amelioration is paralleled by the elimination of macrophages in immunocompetent areas of the spleen and draining lymph nodes, but not locally in the SM. This suggests an influence of the treatment on the immunoregulatory rather than effector, functions of macrophages.
Second-generation image coding (1997)

This article gives an overview of a diverse selection of currently used second-generation image coding techniques. These techniques have been grouped into similar categories in order to allow a direct comparison among the varying methods. An attempt has been made, where possible, to expand upon and clarify the details given by the original authors. The relative merits ans shortcomings of each of the techniques are compared and contrasted.
Linear Side Chains in Benzo[1,2-b:4,5-b′]dithiophene–Thieno[3,4-c]pyrrole-4,6-dione Polymers Direct Self-Assembly and Solar Cell Performance (2013)

While varying the size and branching of solubilizing side chains in π-conjugated polymers impacts their self-assembling properties in thin-film devices, these structural changes remain difficult to anticipate. This report emphasizes the determining role that linear side-chain substituents play in poly(benzo[1,2-b:4,5-b']dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers for bulk heterojunction (BHJ) solar cell applications. We show that replacing branched side chains by linear ones in the BDT motifs induces a critical change in polymer self-assembly and backbone orientation in thin films that correlates with a dramatic drop in solar cell efficiency. In contrast, we show that for polymers with branched alkyl-substituted BDT motifs, controlling the number of aliphatic carbons in the linear N-alkyl-substituted TPD motifs is a major contributor to improved material performance. With this approach, PBDTTPD polymers were found to reach power conversion efficiencies of 8.5% and open-circuit voltages of 0.97 V in BHJ devices with PC71BM, making PBDTTPD one of the best polymer donors for use in the high-band-gap cell of tandem solar cells.
Corticotrophin‐releasing factor, vasopressin and pro‐opiomelanocortin mRNA responses to stress and opiates in the rat. (1988)

1. Rats underwent either: (1) acute or chronic morphine or naloxone administration; (2) simple morphine withdrawal or naloxone-precipitated withdrawal in morphine-dependent animals; or (3) stress from I.P. administration of hypertonic saline. 2. Quantitative in situ hybridization histochemistry was performed using synthetic oligonucleotide probes for corticotrophin-releasing factor (CRF), vasopressin, pro-opiomelanocortin (POMC), dynorphin, enkephalin and oxytocin mRNAs. The paraventricular and supraoptic nuclei were examined in all studies and the arcuate nucleus and pituitary gland in the acute withdrawal study. 3. Neither acute nor chronic morphine administration altered either (a) hypothalamic parvocellular or magnocellular CRF mRNA, or (b) anterior pituitary or pars intermedia POMC mRNA. 4. Naloxone-precipitated morphine withdrawal resulted in a marked increase in parvocellular (but not magnocellular) CRF mRNA within 4 h and levels remained elevated through 24 h. There was no change in arcuate nucleus or pars intermedia POMC mRNA, but in the anterior pituitary there was a delayed increase, significant at 24 h. 5. Simple morphine withdrawal without the use of naloxone did not result in any change in CRF mRNA but there were increases in magnocellular vasopressin and dynorphin mRNA, presumably related to decreased water intake. 6. Intraperitoneal hypertonic saline stress also resulted in a marked accumulation of both parvocellular CRF and vasopressin mRNA without any concomitant change in magnocellular vasopressin mRNA. Increased translation of CRF mRNA was also evidenced by increased immunoreactive CRF detected by immunocytochemistry.
Anionic polymerization of N‐substituted maleimide. II. Polymerization of N‐ethylmaleimide (1988)

Abstract Anionic polymerization of N ‐ethylmaleimide ( N ‐EMI) was carried out with potassium t ‐butoxide, lithium t ‐butoxide, n ‐butyllithium, and ethylmagnesium bromide as initiators in THF and in toluene. An almost quantitative yield of poly( N ‐EMI) was obtained with potassium t ‐butoxide as initiator in THF in a wide range of polymerization temperatures. Initiators possessing lithium as counter cation produced poly( N ‐EMI) in slightly lower yields and ethylmagnesium bromide gave the polymer only in less than 35% yield in THF. As a polymerization reaction solvent, THF was preferable for the polymerization of N ‐EMI compared with toluene with respect to polymer yields. Poly( N ‐EMI) obtained with anionic initiators exerted unimodal molecular weight distribution. From 1 H‐ and 13 C‐NMR spectra of poly( N ‐EMI) anionic polymerization of N ‐EMI with potassium t ‐butoxide was revealed to proceed at carbon–carbon double bond. t ‐Butoxide system was found to have a “living” polymerization character, i.e., the observed average degree of polymerization was in good agreement with the one calculated from the initial molar ratio of N ‐EMI/initiator and the yield of polymer.
MetaboLyzer: A Novel Statistical Workflow for Analyzing Postprocessed LC–MS Metabolomics Data (2013)

Metabolomics, the global study of small molecules in a particular system, has in the past few years risen to become a primary -omics platform for the study of metabolic processes. With the ever-increasing pool of quantitative data yielded from metabolomic research, specialized methods and tools with which to analyze and extract meaningful conclusions from these data are becoming more and more crucial. Furthermore, the depth of knowledge and expertise required to undertake a metabolomics oriented study is a daunting obstacle to investigators new to the field. As such, we have created a new statistical analysis workflow, MetaboLyzer, which aims to both simplify analysis for investigators new to metabolomics, as well as provide experienced investigators the flexibility to conduct sophisticated analysis. MetaboLyzer's workflow is specifically tailored to the unique characteristics and idiosyncrasies of postprocessed liquid chromatography-mass spectrometry (LC-MS)-based metabolomic data sets. It utilizes a wide gamut of statistical tests, procedures, and methodologies that belong to classical biostatistics, as well as several novel statistical techniques that we have developed specifically for metabolomics data. Furthermore, MetaboLyzer conducts rapid putative ion identification and putative biologically relevant analysis via incorporation of four major small molecule databases: KEGG, HMDB, Lipid Maps, and BioCyc. MetaboLyzer incorporates these aspects into a comprehensive workflow that outputs easy to understand statistically significant and potentially biologically relevant information in the form of heatmaps, volcano plots, 3D visualization plots, correlation maps, and metabolic pathway hit histograms. For demonstration purposes, a urine metabolomics data set from a previously reported radiobiology study in which samples were collected from mice exposed to γ radiation was analyzed. MetaboLyzer was able to identify 243 statistically significant ions out of a total of 1942. Numerous putative metabolites and pathways were found to be biologically significant from the putative ion identification workflow.
Outcome of pancreatic cancer patients based on genetic lymph node staging. (2000)

We prospectively assessed the clinical value of genetic staging of lymph node metastasis in patients with pancreatic adenocarcinoma who underwent curative surgery. K-ras gene mutations were detected in the primary tumors in 18 of 25 patients with pancreatic adenocarcinoma. Among these 18 patients, mutated K-ras gene was also found in at least one lymph node in 13 patients. Of these 13 patients, seven had no evidence of histological nodal involvement and six had histological lymph node metastasis. Although there was no significant difference in overall survival rates between the pathological node-negative and -positive patients, overall survival of the five patients with nodes-negative for the mutated K-ras gene were significantly better than that of the 13 patients with genetically metastasis-positive nodes (p<0.001). Furthermore, overall survival of the six patients with genetically metastasis-positive nodes limited to peripancreatic area was significantly better than that of seven patients with genetical metastasis in lymph nodes beyond the peripancreatic areas (p=0.018). These findings suggest that detection of K-ras gene mutations in lymph nodes may be clinically useful to assess the accurate tumor staging and to stratify the patient with pancreatic adenocarcinoma who are at high or low risk for recurrence after curative surgery.
Human Tregs Made Antigen Specific by Gene Modification: The Power to Treat Autoimmunity and Antidrug Antibodies with Precision (2017)

Human regulatory CD4<sup>+</sup> T cells (Tregs) are potent immunosuppressive lymphocytes responsible for immune tolerance and homeostasis. Since the seminal reports identifying Tregs, vast research has been channeled into understanding their genesis, signature molecular markers, mechanisms of suppression, and role in disease. This research has opened the doors for Tregs as a potential therapeutic for diseases and disorders such as multiple sclerosis, type I diabetes, transplantation, and immune responses to protein therapeutics, like factor VIII. Seminal clinical trials have used polyclonal Tregs, but the frequency of antigen-specific Tregs among polyclonal populations is low, and polyclonal Tregs may risk non-specific immunosuppression. Antigen-specific Treg therapy, which uses genetically modified Tregs expressing receptors specific for target antigens, greatly mitigates this risk. Building on the principles of T-cell receptor cloning, chimeric antigen receptors (CARs), and a novel CAR derivative, called B-cell antibody receptors, our lab has developed different types of antigen-specific Tregs. This review discusses the current research and optimization of gene-modified antigen-specific human Tregs in our lab in several disease models. The preparations and considerations for clinical use of such Tregs also are discussed.
Hot topic: Early postpartum treatment of commercial dairy cows with nonsteroidal antiinflammatory drugs increases whole-lactation milk yield (2015)

Previous research has shown that postpartum administration of the nonsteroidal antiinflammatory drug (NSAID) sodium salicylate can increase 305-d milk yield in older dairy cattle (parity 3 and greater). However, in this prior work, sodium salicylate was delivered to cows via the drinking water, a method that does not align well with current grouping strategies on commercial dairy farms. The objective of the current study was to replicate these results on a commercial dairy farm with a simplified treatment protocol and to compare sodium salicylate with another NSAID, meloxicam. Dairy cattle in their second lactation and greater (n=51/treatment) were alternately assigned to 1 of 3 treatments at parturition, with treatments lasting for 3d. Experimental treatments began 12 to 36 h after parturition and were (1) 1 placebo bolus on the first day and 3 consecutive daily drenches of sodium salicylate (125 g/cow per day; SAL); (2) 1 bolus of meloxicam (675 mg/cow) and 3 drenches of an equal volume of water (MEL); or (3) 1 placebo bolus and 3 drenches of water (CON). Blood samples were collected on the first day of treatment, immediately following the last day of treatment, and 7d after the last day of treatment; plasma was analyzed for glucose, β-hydroxybutyrate (BHB), free fatty acids, haptoglobin, and paraoxonase. Milk production, body condition score, reproductive status, and retention in the herd were monitored for 365 d posttreatment, and effects of treatment, parity, days in milk, and interactions were evaluated in mixed effects models. Significance was declared at P<0.05. Whole-lactation milk and protein yields were greater in NSAID-treated cows, although 305-d fat production was not affected. There was a significant interaction of treatment and parity for plasma glucose concentration; MEL increased plasma glucose concentrations compared with CON and SAL in older cows. Sodium salicylate decreased plasma BHB concentration compared with MEL at 7d posttreatment, although no difference was detected immediately following treatment. Haptoglobin concentrations were elevated in SAL cows compared with CON. There was a tendency for CON cows to be removed from the herd more quickly than MEL cows (42 vs. 26% at 365 d posttreatment). Body condition score, concentrations of plasma free fatty acids and paraoxonase, and time to pregnancy were not affected by treatment. These results indicate that NSAID administration in postpartum cows has the potential to be a viable way to improve productivity and potentially longevity in commercial dairies, although further research is necessary to optimize recommendations for producers.
Nonrandom chromosome changes in malignant melanoma. (1983)

Chromosome aberrations were analyzed in 4 cases of malignant melanoma (MM) after disaggregation of the tumors with collagenase and short-term culture. In all cell cultures, the MM cells displayed a typical triangular spindle form. The chromosome number was near-diploid in one case and near-triploid in three cases. A total of 27 abnormal chromosomes were identified with the Giemsa banding technique. By far, the most common types of abnormalities were translocations, followed by deletions and isochromosomes. Chromosomes 1, 6, and 7 were found to be most frequently involved in structural aberrations. Markers originating from chromosomes 1 and 6 were found in all four cases, and abnormalities of chromosome 7 were found in three. Each marker chromosome was unique for a given case; no common markers for two or more cases were found. Based on the present results and an analysis of reports on the chromosomal constitution of MM cells in the literature, we suggest that abnormalities involving chromosomes 6 and 7 may be a characteristic feature of MM. Aberrations of chromosome 1, although common in MM, may be part of a general cytogenetic feature in human neoplasia.