gebhart/patrepeval huggingface dataset:
A New Joining Process for Magnesium Alloys: Rotation Friction Drilling Riveting (2013)

A new joining process for magnesium alloys, rotation friction drilling riveting (RFDR), is proposed in this paper. In RFDR operation, a semitubular rivet with a grip rod and a rivet cap rotating at high speed is brought to contact with the riveted sheets, generating frictional heat between the rivet and riveted sheets, which softens the sheet materials and enables the rivet to be drilled into the sheets under reduced force. While being inserted, the rivet pierces through the top sheet and flares into the bottom sheets due to the action of the cavity die, thereby forming a mechanical interlock between the rivet and riveted sheets. Our studies showed that RFDR of the magnesium alloy sheets could be carried out at room temperature and provided the joints with superior shear strength and fatigue property when compared with self-piercing riveting (SPR). The effects of the operating parameters of the RFDR process on the quality of the joints were also investigated in the study. The results showed that while the rivet rotating speed little affected the shear strength of RFDR joints, the rivet shank length and the downward pressure had a significant influence on the mechanical properties of the RFDR joints. Therefore, it is very important to choose the right rivet shank length and downward pressure for producing RFDR joints with high quality.
Quality Control After Insertion of the Nucleus Contour and Contour Advance Electrode in Adults (2007)

Results of studying the Contour array influenced the surgical procedure that improved surgical ability to perform insertions into the scala tympani by using the Contour Advance array. In addition, a comparison between Contour and Contour Advance electrode demonstrated an improved mechanical behavior of the Contour Advance electrode with a decrease of dislocation rate. The use of the Contour Advance electrode allows a more atraumatic electrode insertion, which is of interest with extending indications and the use of further advanced coding strategies. The intracochlear electrode position with regard to speech performance results demonstrated advantages of scala tympani insertions.
Forced Vital Capacity in Patients with Idiopathic Pulmonary Fibrosis: Test Properties and Minimal Clinically Important Difference (2011)

FVC is a reliable, valid, and responsive measure of clinical status in patients with IPF, and a decline of 2-6%, although small, represents a clinically important difference.
Androgen-induced inhibition of cell proliferation in an androgen-insensitive prostate cancer cell line (PC-3) transfected with a human androgen receptor complementary DNA. (1993)

A full length human androgen receptor complementary DNA was introduced into androgen receptor-negative PC-3 cells to determine if androgen sensitivity could be established in this cell line and to assess what influence, if any, androgen exposure would have on the growth of these cells. The androgen receptor complementary DNA was inserted into pSG5 in the region controlled by the SV40 promoter. This construct was cotransfected with pSR1neo into PC-3 cells and stably transfected cells were selected and screened for the expression of the androgen receptor. Active expression of the receptor was demonstrated by Western blotting using a rabbit anti-androgen receptor antiserum and by [3H]methyltrienolone binding to cytosol extracts. Saturation ligand-binding analysis revealed the presence of a single class, high affinity (Kd = 0.122 nM) androgen-binding site in cytosol extracts of transfected cells but not in extracts from mock-transfected cells. In cells expressing the transfected androgen receptor, androgen decreased the proliferation rate and cloning efficiency and induced a more differentiated phenotype. These results demonstrate that PC-3 cells have retained the mechanisms required to respond to the activated androgen receptor and that the loss of androgen sensitivity in these cells is due to the lack of functional androgen receptor. This also provides a technique for determining whether androgen-resistant tumor cells contain functional androgen receptors or whether androgen sensitivity is due to abnormalities in downstream signaling pathways. The apparent androgen-induced decreased malignant state of these transfected cells suggests new directions for the treatment of prostate cancer.
The Protein Data Bank (1977)

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. alpha-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.
All-fiber chirped pulse amplification using highly-dispersive air-core photonic bandgap fiber (2003)

We show, for the first time to our knowledge, all-fiber chirped pulse amplification using an air-core photonic bandgap fiber. Pulses from a wavelength- and duration-tunable femtosecond/picosecond source at 10 GHz were dispersed in 100 m of dispersion compensating fiber before being amplified in an erbium-doped fiber amplifier and subsequently recompressed in 10 m of the anomalously dispersive photonic bandgap fiber. Pulses as short as 1.1 ps were obtained. As air-core fibers present negligible nonlinearity, the presented configuration can potentially be used to obtain ultra-high pulse peak powers. A study of the air-core fiber dispersion and dispersion slope is also presented.
Circulating levels of leptin, adiponectin, resistin, and ghrelin in inflammatory bowel disease (2006)

Serum levels of adiponectin, resistin, and active ghrelin are increased whereas serum levels of leptin are decreased in patients with IBD. Further studies are needed to elucidate the role of adipocytokines in IBD.
Myelodysplastic Syndromes — Coping with Ineffective Hematopoiesis (2005)

One of the most challenging problems in hematology is the heterogeneous group of disorders that were formally defined as myelodysplastic syndromes by the French–American–British Cooperative Group in 1982. This set of disorders includes idiopathic conditions as well as the secondary or therapy-related forms that develop after exposure to alkylating agents, radiation, or both. Idiopathic myelodysplastic syndromes occur mainly in older persons: the incidence of these syndromes is about 5 per 100,000 persons per year in the general population, but it increases to 20 to 50 per 100,000 persons per year after 60 years of age. Approximately 15,000 new cases are . . .
Use of the coagulase gene typing method for detection of carriers of methicillin-resistant Staphylococcus aureus (1996)

Strains of Staphylococcus aureus can be typed on the basis of the polymorphism of the coagulase gene. DNA fragments generated after amplification by polymerase chain reaction (PCR) of the variable region of this gene and digested with the restriction enzyme HaeIII can be compared by their restriction fragment length polymorphism (RFLP). Seventy-nine of 86 (91.8%) methicillin-resistant S. aureus (MRSA) strains isolated in various hospitals had a characteristic RFLP pattern. This pattern differed from those of 32 methicillin-susceptible S. aureus (MSSA). Only one MSSA shared with MRSA the same RFLP pattern. After modification, we applied this method to the rapid detection of MRSA from 255 nasal swabs from patients hospitalized in intensive care units. When screened by plating on Chapman agar, 55 of these samples contained MRSA, whereas 40/55 yielded the expected restriction profile after amplification by PCR. No DNA was amplified by PCR in 9/55 samples and restriction profiles were uninterpretable in six cases. When compared to culture, the positive and negative predictive values of the PCR test were 100% and 93%, respectively. The specificity was 100% and the sensitivity was 72.7%. Since control of spread of MRSA strains in hospitals is based in part on rapid isolation of carriers, this method which allows detection of epidemic MRSA in nasal swabs within a day could be helpful, though culture would still be necessary to confirm the result.
Edible vaccine protects mice against Escherichia coli heat-labile enterotoxin (LT): potatoes expressing a synthetic LT-B gene (1998)

The authors have designed and constructed a plant-optimize synthetic gene encoding the Escherichia coli heat-labile enterotoxin B subunit (LT-B), for use in transgenic plants as an edible vaccine against enterotoxigenic E. coli. Expression of the synthetic LT-B gene in potato plants under the control of a constitutive promoter yielded increased accumulation of LT-B in leaves and tubers, as compared to the bacterial LT-B gene. The plant-derived LT-B assembled into native pentameric structures as evidenced by its ability to bind ganglioside. The authors demonstrated immunogenicity by feeding mice the raw tubers and comparing the anti-LT-B serum IgG and faecal IgA to that produced in mice gavaged with bacterial LT-B. Mice were fed three weekly doses of 5 g tuber tissue containing either 20 or 50 micrograms LT-B, or gavaged weekly with 5 micrograms of LT-B from recombinant E. coli. One week after the third dose, mice immunized with potato LT-B had higher levels of serum and mucosal anti-LT-B than those gavaged with bacterial LT-B. Mice were challenged by oral administration of 25 micrograms LT, and protection assessed by comparing the gut/carcass mass ratios. Although none of the mice were completely protected, the higher dose potato vaccine compared favourably with the bacterial vaccine. These findings show that an edible vaccine against E. coli LT-B is feasible.
Near optimum error correcting coding and decoding: turbo-codes (1996)

This paper presents a new family of convolutional codes, nicknamed turbo-codes, built from a particular concatenation of two recursive systematic codes, linked together by nonuniform interleaving. Decoding calls on iterative processing in which each component decoder takes advantage of the work of the other at the previous step, with the aid of the original concept of extrinsic information. For sufficiently large interleaving sizes, the correcting performance of turbo-codes, investigated by simulation, appears to be close to the theoretical limit predicted by Shannon.
Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice (2007)

For a significant fraction of mRNAs, their expression is regulated by other RNAs, including cis natural antisense transcripts (cis-NATs) that are complementary mRNAs transcribed from opposite strands of DNA at the same genomic locus. The regulatory mechanism of mRNA expression by cis-NATs is unknown, although a few possible explanations have been proposed. To understand this regulatory mechanism, we conducted a large-scale analysis of the currently available data and examined how the overlapping arrangements of cis-NATs affect their expression level. Here, we show that for both human and mouse the expression level of cis-NATs decreases as the length of the overlapping region increases. In particular, the proportions of the highly expressed cis-NATs in all cis-NATs examined were approximately 36 and 47% for human and mouse, respectively, when the overlapping region was <200 bp. However, both proportions decreased to virtually zero when the overlapping regions were >2000 bp in length. Moreover, the distribution of the expression level of cis-NATs changes according to different types of the overlapping pattern of cis-NATs in the genome. These results are consistent with the transcriptional collision model for the regulatory mechanism of gene expression by cis-NATs.
Stereocontrolled Synthesis of a Sphingomyelin Methylene Analogue as a Sphingomyelinase Inhibitor (2000)

Efficient synthesis of a sphingomyelin methylene analogue, which was designed as a sphingomyelinase inhibitor, was stereoselectively achieved. The Hofmann rearrangement of the α-hydroxyethyl-β-hydroxy amide 4 followed by the intramolecular oxazolidinone ring formation was one of the key steps.
Augmented Reality Tools for Enhanced Structural Inspection (2017)

To date, the tools available to structural inspectors to perform structural inspections have been very limited. In many cases inspectors are limited to using their eyes, ears, a tape measure and a hammer to perform an inspection. Notes are taken using a pad of paper and a pencil. In some cases, a tablet computer might be used to take notes along with a digital camera for documentation. Unfortunately, these techniques are clumsy and result in very few data points being measured and recorded. In this work, we will focus on developing the conceptual design for novel structural inspection tools for structural inspection applications based on emerging augmented reality technology. Augmented reality technology allows for holograms to be overlaid on the real world. It represents an exciting new way for inspectors to both collect, interact with, visualize, and analyze inspection data. The HoloLens allows a hands-free structural inspection and measurement technique minimizing time and challenges. The experiments conducted with the HoloLens for taking measurements and benchmarking the obtained measurements are shown in this study. It is proved that measurements taken from up to 20 feet distance, in and out of the line of sight, have less than 2% error compared to the actual measurement. Further applications of the HoloLens in the field of structural inspection are also discussed in this study.
Monoclonal antibodies against human milk‐fat globule membranes detecting differentiation antigens of the mammary gland and its tumors (1984)

Mouse monoclonal antibodies have been raised against human milk-fat globule membranes (HMFGM) to obtain reagents for mammary tumor diagnosis. A panel of 17 anti-HMFGM antibodies was selected for further investigation. Antibody-blocking studies indicated that with these antibodies at least nine different non-overlapping epitopes could be distinguished on six different molecules, MAM-1 to MAM-6. Electron microscopic studies of the cellular localization of the antigens detected by some of these antibodies revealed that they were present on the cell membrane mainly, on the microvilli, lining intercellular and intracytoplasmic lumina. The reactivity of the antibodies was studied on normal and tumor tissues and on in vitro cell lines. All antibodies reacted with the resting mammary gland while eight antibodies also bound to breast tumors. None of the antibodies was specific for the mammary gland or its tumors only, but most antibodies also reacted with other epithelial cells, especially of secretory tissues. When tested on a variety of cell lines a distribution reflecting the tissue distribution could be demonstrated. One of the antibodies reacted with nearly all carcinomas and their metastases and did not react with lymphomas, sarcomas, neuroblastomas, melanomas or nervous system tumors. The specificity of the antibodies, tested individually, was not sufficient for further differential diagnosis of the carcinomas, but when some of these antibodies were used in a panel they contribute to an important improvement of the diagnosis.
In vitro analysis of promoter activity in Müller cells. (2008)

In this study, we demonstrate that computational and empirical methods, when used in combination, can efficiently identify short promoters that are active in cultured Müller cells. In addition, the pFTM3GW vector can be used to study the effects of combined promoter elements. We anticipate that these methods will expedite the design and testing of synthetic/chimeric promoter constructs that should be useful for both in vitro and in vivo applications.
A hybrid recommendation approach for hierarchical items (2010)

Recommender systems aim to recommend items that are likely to be of interest to the user. In many business situations, complex items are described by hierarchical tree structures, which contain rich semantic information. To recommend hierarchical items accurately, the semantic information of the hierarchical tree structures must be considered comprehensively. In this study, a new hybrid recommendation approach for complex hierarchical tree structured items is proposed. In this approach, a comprehensive semantic similarity measure model for hierarchical tree structured items is developed. It is integrated with the traditional item-based collaborative filtering approach to generate recommendations.
A Novel Lyn-Binding Peptide Inhibitor Blocks Eosinophil Differentiation, Survival, and Airway Eosinophilic Inflammation1, 2 (1999)

Receptor antagonists block all receptor-coupled signaling pathways indiscriminately. We introduce a novel class of peptide inhibitors that is designed to block a specific signal from a receptor while keeping other signals intact. This concept was tested in the model of IL-5 signaling via Lyn kinase. We have previously mapped the Lyn-binding site of the IL-5/GM-CSF receptor common beta (beta c) subunit. In the present study, we designed a peptide inhibitor using the Lyn-binding sequence. The peptide was N-stearated to enable cellular internalization. The stearated peptide blocked the binding of Lyn to the beta c receptor and the activation of Lyn. The lipopeptide did not affect the activation of Janus kinase 2 or its association with beta c. The inhibitor blocked the Lyn-dependent functions of IL-5 in vitro (e.g., eosinophil differentiation from stem cells and eosinophil survival). It did not affect eosinophil degranulation. When applied in vivo, the Lyn-binding peptide significantly inhibited airway eosinophil influx in a mouse model of asthma. The lipopeptide had no effect on basophil histamine release or on the proliferation of B cells and T cells. To our knowledge, this is the first report on an inhibitor of IL-5 that blocks eosinophil differentiation, survival, and airway eosinophilic inflammation. This novel strategy to develop peptide inhibitors can be applied to other receptors.
In vitro and in vivo properties of a fully human IgG1 monoclonal antibody that combats multidrug resistant Pseudomonas aeruginosa (2012)

The development of an anti-bacterial drug in the form of a monoclonal antibody (mAb) targeting an exposed virulence factor, represents an innovative therapeutic strategy. Consequently, a fully human IgG1 mAb (LST-007) targeting Pseudomonas aeruginosa (PA) flagellin type b was recombinantly expressed and characterized in vitro and in an infection model driven by a multidrug resistant (MDR) PA strain. LST-007 demonstrated a highly specific binding towards whole PA bacteria harboring flagellin type b and its recombinant counterpart, with a K(D) of 7.4x10(-10) M. In bioactivity assays, LST-007 or titers of Cmax sera derived from pharmacokinetic studies, markedly attenuated PA motility in an equipotent manner. In vivo, parenteral LST-007 (20 mg/kg) given as a single or double-dosing paradigm post-infection, afforded survival (up to 75% at Day 7) in a lethal model of pneumonia driven by the intratracheal (i.t.) instillation of an LD(80) of the MDR PA isolate. This protective effect was markedly superior to that of imipenem (30% survival at Day 7) and totally devoid with an irrelevant, human isotype mAb. These data lay credence that LST-007 may be a valuable adjunct to the limited list of anti-bacterials that can tackle MDR PA strains, thereby warranting its continued development for eventual clinical evaluation.
Analysis of repeatability in spotted cDNA microarrays (2002)

We report a strategy for analysis of data quality in cDNA microarrays based on the repeatability of repeatedly spotted clones. We describe how repeatability can be used to control data quality by developing adaptive filtering criteria for microarray data containing clones spotted in multiple spots. We have applied the method on five publicly available cDNA microarray data sets and one previously unpublished data set from our own laboratory. The results demonstrate the feasibility of the approach as a foundation for data filtering, and indicate a high degree of variation in data quality, both across the data sets and between arrays within data sets.
Binding assay and preliminary X-ray crystallographic analysis of ACTIBIND, a protein with anticarcinogenic and antiangiogenic activities (2007)

ACTIBIND is a T2 RNase extracellular glycoprotein produced by the mould Aspergillus niger B1 (CMI CC 324626) that possesses anticarcinogenic and antiangiogenic activities. ACTIBIND was found to be an actin-binding protein that interacts with rabbit muscle actin in a 1:2 molar ratio (ACTIBIND:actin) with a binding constant of 16.17 x 10(4) M(-1). Autoclave-treated ACTIBIND (EI-ACTIBIND) lost its RNase activity, but its actin-binding ability was conserved. ACTIBIND crystals were grown using 20% PEG 3350, 0.2 M ammonium dihydrogen phosphate solution at room temperature (293 K). One to four single crystals appeared in each droplet within a few days and grew to approximate dimensions of 0.5 x 0.5 x 0.5 mm after about two weeks. Diffraction studies of these crystals at low temperature (100 K) indicated that they belong to the P3(1)21 space group, with unit-cell parameters a = 78, b = 78, c = 104 A.
A Simian Strain of Hepatitis A Virus, AGM-27, Functions as an Attenuated Vaccine for Chimpanzees (1996)

The AGM-27 strain OF hepatitis A virus (HAV) was originally isolated from an African green monkey with hepatitis and appears to represent a true simian strain. The virus caused acute hepatitis after intravenous inoculation into African green monkeys, rhesus monkeys, and marmosets. Cynomolgus monkeys inoculated with the virus did not develop hepatitis, probably because of prior exposure to HAV. Chimpanzees inoculated with a high dose of the virus did not develop signs of hepatitis, although the virus replicated and the animals seroconverted. Marmosets and chimpanzees convalescent from infection with the AGM-27 strain of HAV were rechallenged with the virulent HM-175 strain of human HAV. They were partially or totally protected from disease.