gebhart/patrepeval huggingface dataset:
Pivotal Role of the CC Chemokine, Macrophage-Derived Chemokine, in the Innate Immune Response (2000)

Macrophage-derived chemokine (MDC), a recently identified CC chemokine, has been regarded to be involved in chronic inflammation and dendritic cell and lymphocyte homing. In this study, we demonstrate a pivotal role for MDC during experimental sepsis induced by cecal ligation and puncture (CLP). Intraperitoneal administration of MDC (1 microg/mouse) protected mice from CLP-induced lethality. The survival was accompanied by increased number of peritoneal macrophages and decreased recovery of viable bacteria from the peritoneum and peripheral blood. In addition, mice treated with an i.p. injection of MDC cleared bacteria more effectively than those in the control when 3 x 108 CFU live Escherichia coli was i.p. inoculated. Endogenous MDC was detected in the peritoneum after CLP, and neutralization of the MDC with anti-MDC Abs decreased CLP-induced recruitment of peritoneal macrophages and increased the recovery of viable bacteria from the peritoneum and peripheral blood. MDC blockade was deleterious in the survival of mice after CLP. In vitro, MDC enhanced the phagocytic and killing activities of peritoneal macrophages to E. coli and induced both a respiratory burst and the release of lysozomal enzyme from macrophages. Furthermore, MDC dramatically ameliorated CLP-induced systemic tissue inflammation as well as tissue dysfunction, which were associated in part with decreased levels of TNF-alpha, macrophage inflammatory proteins-1alpha and -2, and KC in specific tissues. Collectively, these results indicate novel regulatory activities of MDC in innate immunity during sepsis and suggest that MDC may aid in an adjunct therapy in sepsis.
Function of a Conserved Loop of the β-Domain, Not Involved in Thiamin Diphosphate Binding, in Catalysis and Substrate Activation in Yeast Pyruvate Decarboxylase (2006)

The X-ray crystal structure of pyruvamide-activated yeast pyruvate decarboxylase (YPDC) revealed a flexible loop spanning residues 290 to 304 on the beta-domain of the enzyme, not seen in the absence of pyruvamide, a substrate activator surrogate. Site-directed mutagenesis studies revealed that residues on the loop affect the activity, with some residues reducing k(cat)/K(m) by at least 1000-fold. In the pyruvamide-activated form, the loop located on the beta domain can transfer information to the active center thiamin diphosphate (ThDP) located at the interface of the alpha and gamma domains. The sigmoidal v(0)-[S] curve with wild-type YPDC attributed to substrate activation is modulated for most variants, but is not abolished. Pre-steady-state stopped-flow studies for product formation on these loop variants provided evidence for three enzyme conformations connected by two transitions, as already noted for the wild-type YPDC at pH 5.0 [Sergienko, E. A., and Jordan, F. (2002) Biochemistry 41, 3952-3967]. (1)H NMR analysis of the intermediate distribution resulting from acid quench [Tittmann et al. (2003) Biochemistry 42, 7885-7891] with all YPDC variants indicated that product release is rate limiting in the steady state. Apparently, the loop is not solely responsible for the substrate activation behavior, rather it may affect the behavior of residue C221 identified as the trigger for substrate activation. The most important function of the loop is to control the conformational equilibrium between the "open" and "closed" conformations of the enzyme identified in the pyruvamide-activated structure [Lu et al. (2000) Eur. J. Biochem. 267, 861-868].
Decline in Fish Consumption Among Pregnant Women After a National Mercury Advisory (2003)

In Brief OBJECTIVE A well-publicized January 2001 federal advisory recommended that pregnant women limit consumption of certain fish because of concerns about mercury contamination. We endeavored to estimate the extent to which pregnant women changed fish consumption habits after dissemination of this national advisory. METHODS We performed interrupted time series analysis of data from a cohort of pregnant women (2235 who completed at least one dietary questionnaire) visiting obstetric offices in a multispecialty group practice in eastern Massachusetts, surveyed before the advisory from April 1999 through December 2000 and after the advisory from April 2001 through February 2002. Main outcome measures were consumption of total fish and of four fish types: canned tuna, dark meat fish, shellfish, and white meat fish. Subjects reported fish consumption on semiquantitative food frequency questionnaires administered at each trimester of pregnancy. RESULTS We observed diminished consumption of dark meat fish, canned tuna, and white meat fish after the national mercury advisory. These decreases resulted in a reduction in total fish consumption of approximately 1.4 servings per month (95% confidence interval 0.7, 2.0) from December 2000 to April 2001, with ongoing declines through the end of the study period. There was no change in shellfish intake. CONCLUSION After dissemination of federal recommendations, pregnant women in this cohort reported reduced consumption of fish, including tuna, dark meat fish, and white meat fish. Because these fish may confer nutritional benefits to mother and infant, public health implications of these changes remain unclear. Pregnant women reported reduced consumption of fish after dissemination of a federal advisory about the potential risks from mercury in seafood.
Multiple Spitz nevi after allogeneic hematopoietic stem cell transplantation (2018)

Spitz nevus commonly appears as a solitary lesion. A 12-year-old male patient presented with a 6-month history of several pigmented lesions on his trunk and lower extremities. He had undergone chemoradiotherapy and unrelated umbilical cord blood transplantation against recurring acute lymphoblastic leukemia for 6 years. After that, several pigmented lesions abruptly developed on his trunk and lower extremities, and the number of those increased significantly. Pathologically, the diagnosis of multiple Spitz nevi was made. In a clinical correlation, we diagnosed multiple Spitz nevi resulting from such an immunocompromised condition. This is the first description of clinical, dermoscopic, and histopathologic features of multiple Spitz nevi in the hematopoietic cell transplantation (HSCT) recipient child.
Smoothing and Differentiation of Data by Simplified Least Squares Procedures. (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSmoothing and Differentiation of Data by Simplified Least Squares Procedures.Abraham. Savitzky and M. J. E. GolayCite this: Anal. Chem. 1964, 36, 8, 1627–1639Publication Date (Print):July 1, 1964Publication History Published online1 May 2002Published inissue 1 July 1964https://pubs.acs.org/doi/10.1021/ac60214a047https://doi.org/10.1021/ac60214a047research-articleACS PublicationsRequest reuse permissionsArticle Views36629Altmetric-Citations14831LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Phase I Trial of Continuous Infusion Anti-Mesothelin Recombinant Immunotoxin SS1P (2009)

As a single agent by continuous infusion, recombinant immunotoxin SS1P was well tolerated up to 25 microg/kg/d x10 and showed evidence of modest clinical activity. Continuous infusion showed no significant advantage over bolus dosing, and further clinical development of SS1P is proceeding by bolus dosing in combination with chemotherapy.
Practical aspects of fluorescent staining for proteomic applications (2001)

SYPRO Orange and SYPRO Ruby staining methods, modified for use with large-format two dimensional (2-D) gels, are compared to the manufacturer's recommended protocols to determine sensitivity and reproducibility of the new methods. This study examines the critical aspects of fixation, washing, and staining to develop an optimized fluorescent staining method. It was determined that careful control of sodium dodecyl sulfate (SDS) levels and pH in the gel was critical for successful staining with SYPRO Orange. Overnight fixation in 40% ethanol/2% acetic acid/0.0005% SDS preserved protein content, eliminated ampholyte-generated staining artifacts, and had no detrimental effects on staining. Three one-hour washes in 2% acetic acid/0.0005% SDS, followed by staining with SYPRO Orange diluted 1:5,000 with washing solution for 3 or more hours, produced high sensitivity, low background images using a STORM 860 laser scanner. Gels viewed two years after staining showed no significant changes with respect to the initial protein patterns, and allowed successful mass spectrometric postgel characterization of protein spots. Protocol changes applied to SYPRO Ruby staining improved the contrast of STORM 860-generated images, but had little impact on staining sensitivity. A comparison of the cost benefits of staining with SYPRO Orange vs. SYPRO Ruby is also discussed.
Cell-free cloning using φ29 DNA polymerase (2005)

We describe conditions for rolling-circle amplification (RCA) of individual DNA molecules 5-7 kb in size by >10(9)-fold, using phi29 DNA polymerase. The principal difficulty with amplification of small amounts of template by RCA using phi29 DNA polymerase is "background" DNA synthesis that usually occurs when template is omitted, or at low template concentrations. Reducing the reaction volume while keeping the amount of template fixed increases the template concentration, resulting in a suppression of background synthesis. Cell-free cloning of single circular molecules by using phi29 DNA polymerase was achieved by carrying out the amplification reactions in very small volumes, typically 600 nl. This procedure allows cell-free cloning of individual synthetic DNA molecules that cannot be cloned in Escherichia coli, for example synthetic phage genomes carrying lethal mutations. It also allows cell-free cloning of genomic DNA isolated from bacteria. This DNA can be sequenced directly from the phi29 DNA polymerase reaction without further amplification. In contrast to PCR amplification, RCA using phi29 DNA polymerase does not produce mutant jackpots, and the high processivity of the enzyme eliminates stuttering at homopolymer tracts. Cell-free cloning has many potential applications to both natural and synthetic DNA. These include environmental DNA samples that have proven difficult to clone and synthetic genes encoding toxic products. The method may also speed genome sequencing by eliminating the need for biological cloning.
Purification and Characterization of an Esterase Involved in Cellulose Acetate Degradation byNeisseria siccaSB (1999)

An esterase catalyzing the hydrolysis of acetyl ester moieties in cellulose acetate was purified 1,110-fold to electrophoretic homogeneity from the culture supernatant of Neisseria sicca SB, which can assimilate cellulose acetate as the sole carbon and energy source. The purified enzyme was a monomeric protein with a molecular mass of 40 kDa and the isoelectric point was 5.3. The pH and temperature optima of the enzyme were 8.0-8.5 and 45 degrees C. The enzyme catalyzed the hydrolysis of acetyl saccharides, p-nitrophenyl esters of short-chain fatty acids, and was slightly active toward aliphatic and aromatic esters. The K(m) and Vmax for cellulose acetate (degree of substitution, 0.88) and p-nitrophenyl acetate were 0.0162% (716 microM as acetyl content in the polymer) and 36.0 microM, and 66.8 and 39.1 mumol/min/mg, respectively. The enzyme was strongly inhibited by phenylmethylsulfonyl fluoride and diisopropyl fluorophosphate, which indicated that the enzyme was a serine esterase.
Protein disulfide isomerase is both an enzyme and a chaperone (1993)

Protein disulfide isomerase (PDI) catalyzes the formation of native disulfides of peptide chains from either the reduced form or randomly joined disulfides. So that thiols situated at distant parts of the polypeptide chain can be joined together to form the native disulfides, the polypeptide chain has to be folded, at least to some extent, into the native conformation. It is suggested that PDI promotes folding of the chains as well as formation of the disulfides and plays a role similar to the chaperones in the folding process. PDI is known to be a multifunctional protein and capable of nonspecific peptide binding. These properties are closely connected to its possible function as a chaperone. Thioredoxin, which has an active site sequence similar to that of PDI but lacks the property of peptide binding, is much less efficient as a disulfide isomerase.
Gene transfer to the patellar tendon (1997)

Growth factors have the potential to enhance native repair responses in ligamentous lesions. However, methods for applying these cytokines to sites of injury for extended periods are lacking. We suggest that local transfer of genes which encode the relevant healing factors merits investigation as a potential solution to this problem. In the present study, the retroviral vectors MFG lacZ and BAG lacZ neo(r) and adenovirus LacZ were evaluated for their ability to deliver genes to cells of ligamentous origin. The posterior and anterior cruciate ligaments, medial collateral ligament, semitendinosus tendon and patellar tendon were harvested from New Zealand white rabbits. Cells grown from these tissues were then investigated for their susceptibility to genetic alteration by these vectors in vitro. Based upon their ability to convert cells in culture to a lacZ(+) phenotype, adenovirus was the most effective vector in short-term experiments. However, expression was transient. Although retrovirus gave lower initial transduction efficiencies, the percentage of transduced cells could be increased by the use of the selectable marker gene neo(r). In an in vivo marker study, we injected adenovirus into the rabbit patellar tendon. Transduced cells could be observed preferentially in the subsynovial layer at a declining frequency over a 6-week period. The allogeneic transplantation of in vitro retrovirally transduced fibroblasts into the patellar tendon resulted in a greater number of transduced cells. Although the number of lacZ(+) cells declined with time, positive cells were still present 6 weeks after transplantation. Furthermore, the transplanted cells, unlike cells transduced in situ with adenovirus, migrated from the injection site and integrated into the crimp of the tendon.
Enhancer-driven membrane markers for analysis of nonautonomous mechanisms reveal neuron–glia interactions in Drosophila (2011)

Extrinsic factors and the interactions of neurons with surrounding tissues are essential for almost every aspect of neuronal development. Here we describe a strategy of gene expression with an independent enhancer-driven cellular marker (GEEM) for studying roles of cell-cell interactions and extrinsic factors in the development of the Drosophila nervous system. Key to this strategy is robust expression of enhancer-driven transgenic markers in specific neurons. To this end, we have created vectors to achieve bright and even labeling of neuronal processes, easy cloning of enhancer elements, and efficient and flexible generation of transgenic animals. We provide examples of enhancer-driven membrane markers for specific neurons in both the peripheral and central nervous systems and their applications in the study of neuronal projections and connections in the Drosophila brain. We further applied GEEM to examine the wrapping of sensory neuron somas by glia during embryonic and larval stages, and neuron-glia interaction during dendrite pruning in live animals, leading to the discovery that glia play critical roles in the severing and degradation of proximal dendrites. The GEEM paradigm should be applicable to the studies of both cell-autonomous and nonautonomous regulations of any cell type.
Abstract 16179: Rap-011, a Murine Ortholog of ActRIIA-Fc (Sotatercept), Improves Pulmonary Hemodynamics and Restores Right Ventricular Structure and Function in a Preclinical Model of Severe Angio-Obliterative Pulmonary Arterial Hypertension (2018)

Introduction: Novel therapies that repair remodeled pulmonary arteries, improve pulmonary hemodynamics and restore right ventricular (RV) structure and function are warranted in pulmonary arterial ...
$gen$CNN: A Convolutional Architecture for Word Sequence Prediction (2015)

We propose a novel convolutional architecture, named $gen$CNN, for word sequence prediction. Different from previous work on neural network-based language modeling and generation (e.g., RNN or LSTM), we choose not to greedily summarize the history of words as a fixed length vector. Instead, we use a convolutional neural network to predict the next word with the history of words of variable length. Also different from the existing feedforward networks for language modeling, our model can effectively fuse the local correlation and global correlation in the word sequence, with a convolution-gating strategy specifically designed for the task. We argue that our model can give adequate representation of the history, and therefore can naturally exploit both the short and long range dependencies. Our model is fast, easy to train, and readily parallelized. Our extensive experiments on text generation and $n$-best re-ranking in machine translation show that $gen$CNN outperforms the state-of-the-arts with big margins.
Spontaneous axonal regeneration after optic nerve injury in adult rat (1999)

Optic nerves of adult rats were crushed 2 mm behind the eye to examine the ability of retinal ganglion cells (RGCs) to regenerate their axons. Some animals were treated with the immunophilin ligands FK 506 or GPI 1046 for up to 4 weeks. After 10 days to 16 months, regenerating RGC axons were visualized using anterograde tracing and/or electron microscopy. A small proportion of RGC axons regenerated across the lesion site and grew very slowly along the entire optic nerve. Immunophilin ligands had no obvious effect. The regenerating axons were about 0.2 microm in diameter, and usually in clusters surrounded by astrocyte processes. Thus, some CNS axons can spontaneously regenerate long distances within degenerate white matter and this slow regeneration is not accelerated by immunophilin ligands.
Antibodies to the A27 Protein of Vaccinia Virus Neutralize and Protect against Infection but Represent a Minor Component of Dryvax Vaccine–Induced Immunity (2007)

The smallpox vaccine Dryvax, which consists of replication-competent vaccinia virus, elicits antibodies that play a major role in protection. Several vaccinia proteins generate neutralizing antibodies, but their importance for protection is unknown. We investigated the potency of antibodies to the A27 protein of the mature virion in neutralization and protection experiments and the contributions of A27 antibodies to Dryvax-induced immunity. Using a recombinant A27 protein (rA27), we confirmed that A27 contains neutralizing determinants and that vaccinia immune globulin (VIG) derived from Dryvax recipients contains reactivity to A27. However, VIG neutralization was not significantly reduced when A27 antibodies were removed, and antibodies elicited by an rA27 enhanced the protection conferred by VIG in passive transfer experiments. These findings demonstrate that A27 antibodies do not represent the major fraction of neutralizing activity in VIG and suggest that immunity may be augmented by vaccines and immune globulins that include strong antibody responses to A27.
Visually-Guided Balloon Catheter Ablation of Atrial Fibrillation (2009)

This study establishes the feasibility of a novel paradigm for AF ablation: direct visualization to guide catheter ablation of the left atrial-PV junction.
Radial-Flow Affinity Chromatography for Trypsin Purification (1990)

The dynamic performance of a radial-flow affinity chromatographic system for trypsin purification has been studied experimentally and theoretically. A mathematical model, which considers both axial dispersion in the mobile phase and pore diffusion inside the fiber, has been developed for simulation and parameter estimation. Based on this model, a design equation has been derived for scale-up of column operation. The design equation employs the concept of volume equivalent of a theoretical stage (VETS) instead of height equivalent of a theoretical plate (HETP) commonly used in the axial-flow chromatography. Experiments from the frontal elution approach were designed and tested for verification of this design equation. A methodology of estimating system parameters from breakthrough experiments was also proposed and applied to the model system.
Antisense oligonucleotide intralesional therapy for human PC-3 prostate tumors carried in athymic nude mice (1996)

Previously we reported hemorrhagic necrosis in human-derived PC-3 prostate tumors, in athymic nude mice, produced by the intralesional injection of antisense oligonucleotides (oligos) directed against mRNAs encoding transforming growth factor-alpha (TGF-alpha) and its target, the epidermal growth factor receptor (EGFR). We now describe our experience with these oligos in treating additional mice with various doses and modes of administration. During prolonged treatment, a dose-response effect was observed, with the optimal dosage consisting of the combination of 400 micrograms of each oligo. Although responses varied, based upon amount and how oligos were administered, we found that tumors were best treated when initially less than 156 mm3. Intralesional inoculations produced necrosis and yielded responses, ranging from complete response (CR) or cure to partial responses (PR) in 9 of 12 tumors treated with full dose (400 micrograms of each oligo) and 1 of 1 treated with 800 micrograms of each oligo, against a large tumor. Included among the 9 positive responses with full-dose administration were 2 tumors that regressed (one completely). A single tumor treated with twice (2X) the normal dosage (800 micrograms of each oligo) also regressed. A single tumor treated with half (1/2) dose (200 micrograms of each) progressed similar to controls, as did 3 of 12 treated with the full dose. Limited experience with ALZET diffusion pumps gave CR (1 of 3) or PR (2 of 3) in 100% of tumors treated (including one mouse cured of multiple tumors in a five day period). It appears that multiple inoculations consisting of 400 micrograms of each oligo is most effective against these tumors, particularly when administered against tumors of <156 mm3 in initial size.