gebhart/patrepeval huggingface dataset:
Expression and secretion of an assembled tetrameric CH2-deleted antibody in E. coli (1992)

We have expressed in E. coli a functional assembled antibody variant that is secreted into the media. The antibody variant is a CH2-deleted chimeric antibody 14.18, which was previously shown to be a potentially useful reagent for radioimmunodetection of human tumors. The bacterial expression vector contains a dicistronic unit comprised of a L-chain cDNA and a CH2-deleted H-chain cDNA. For translocation across the bacterial membranes, we have replaced the natural signal peptides of the H and L chains with the signal peptide of the bacterial protein pectate lyase B. When expressed in the JM105 host under the control of the trp-lac promoter, the products were secreted into the M9 growth media to about 350 micrograms/L. The secreted antibody, which can be readily purified from the media without any denaturation or renaturation steps, retains antigen-binding activity. SDS-PAGE and nondenaturing size exclusion high-pressure liquid chromatography showed that it is a mixture of assembled HL and fully assembled H2L2. In H2L2, inter-H chain disulfide bonds are not formed, and the two HL half-molecules are likely held together by the trans interaction between the two CH3 domains.
Eukaryotic Ribonuclease P: A Plurality of Ribonucleoprotein Enzymes (2002)

Ribonuclease P (RNase P) is an essential endonuclease that acts early in the tRNA biogenesis pathway. This enzyme catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs. RNase P activities have been identified in Bacteria, Archaea, and Eucarya, as well as organelles. Most forms of RNase P are ribonucleoproteins, i.e., they consist of an essential RNA subunit and protein subunits, although the composition of the enzyme in mitochondria and chloroplasts is still under debate. The recent purification of the eukaryotic nuclear RNase P has demonstrated a significantly larger protein content compared to the bacterial enzyme. Moreover, emerging evidence suggests that the eukaryotic RNase P has evolved into at least two related nuclear enzymes with distinct functions, RNase P and RNase MRP. Here we review current information on RNase P, with emphasis on the composition, structure, and functions of the eukaryotic nuclear holoenzyme, and its relationship with RNase MRP.
Induced Cell Clustering Enhances Islet β Cell Formation from Human Cultures Enriched for Pancreatic Ductal Epithelial Cells (2006)

A better understanding of the culture conditions that stimulate in vitro beta-cell differentiation from islet precursors would be useful for optimizing the production of tissue-engineered islets. In this study, high- and low-adherent substrates and high- and low-serum media were used to control the clustering of human pancreatic ductal epithelial cells and to determine its effect on their transdifferentiation to beta cells. While the initial epithelial cell cultures were devoid of any beta cells as assessed by dithizone staining, dithizone+ cells were generated during the next 3 weeks under all culture conditions. Although the rate of transdifferentiation was low, a approximately 4-fold greater number and percentage of dithizone+ cells were generated following 23-24 days of culture in the least adherent conditions (low-serum medium, low-adherent substrate), which stimulated cell clustering to the highest degree. Insulin immunohistochemistry data correlated well with the dithizone data (r(2) = 0.99), evidence that dithizone is a reliable measure of insulin+ cells. The preferential distribution of the dithizone+ cells to regions of cell aggregation and the increased efficiency of transdifferentiation in conditions that promote cell clustering suggest that cell-cell interactions and/or cell shape changes are important to the transdifferentiation of adult pancreatic ductal epithelial cells to beta cells in vitro.
Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany (2011)

Our findings suggest that horizontal genetic exchange allowed for the emergence of the highly virulent Shiga-toxin-producing enteroaggregative E. coli O104:H4 strain that caused the German outbreak. More broadly, these findings highlight the way in which the plasticity of bacterial genomes facilitates the emergence of new pathogens.
Growth-inhibitory Effects of the Red Alga Gelidium amansii on Cultured Cells (2004)

The objective of this study was to investigate the effects of Gelidium amansii, an edible red agar cultivated off the northeast coast of Taiwan, on the growth of two lines of cancer cells, murine hepatoma (Hepa-1) and human leukemia (HL-60) cells, as well as a normal cell line, murine embryo fibroblast cells (NIH-3T3). The potential role of G. amansii on the induction of apoptosis was also examined. The results indicated that all extracts from G. amansii, including phosphate-buffered saline (PBS) and methanol extracts from dried algae as well as the dimethyl sulfoxide (DMSO) extract from freeze-dried G. amansii agar, inhibited the growth of Hepa-1 and NIH-3T3 cells, but not the growth of HL-60 cells. Annexin V-positive cells were observed in methanol and DMSO extract-treated, but not PBS extract-treated Hepa-1 and NIH-3T3 cells, suggesting that the lipid-soluble extracts of G. amansii induced apoptosis. In summary, extracts of G. amansii from various preparations exhibited antiproliferative effects on Hepa-1 and NIH-3T3 cells, and apoptosis may play a role in the methanol and DMSO extract-induced inhibitory effects. However, the antiproliferative effects of PBS extracts was not through apoptosis. Moreover, the growth-inhibitory effects of G. amansii were not specific to cancer cells.
Seventeenth Canadian Geotechnical Colloquium: The effect of cohesion loss and stress path on brittle rock strength (1997)

Stress-strain curves for brittle rocks show three characteristic stress levels: crack initiation, long-term strength, and peak strength. Damage-controlled testing at low confining stresses has shown that the long-term and peak strengths are sensitive to the amount of induced damage, i.e., the greater the amount of damage, the lower the long-term and peak strengths. These tests also showed that the brittle-failure process is characterized by a loss of cohesion as friction is mobilized. Excavation of a circular test tunnel in massive brittle rock resulted in failure around the tunnel. The back-calculated strength for the failed rock around the tunnel is approximately one-half of that measured in laboratory tests. Crack-induced damage of Lac du Bonnet granite, both in the laboratory and in situ, begins when the load exceeds approximately one-third of the unconfined compressive strength. However, the stress level associated with failure is a function of loading path. In the laboratory, where the loading path monotonically increases, the ultimate strength of an unconfined sample is 225 MPa. Numerical studies suggest that in situ the loading path around the tunnel is more complex, involving stress increase and decrease and stress rotation. For this loading path, failure initiates at a stress between 100 and 120 MPa. Conventional frictional failure criteria did not adequately predict the extent of brittle failure measured around the circular tunnel. The results from the damage-controlled laboratory tests and the microseismic monitoring carried out during tunnel construction indicate a constant-deviatoric-stress criterion is a reliable indicator for predicting the onset of damage. This criterion was also found to give a reasonable prediction for the maximum depth of failure around the test tunnel. The fundamental assumption in the constant-deviatoric-stress criterion is that at low confining stresses, such as those which occur around underground openings, the brittle-failure process is dominated by cohesion loss.
Intracoronary Angiotensin II Potentiates Coronary Sympathetic Vasoconstriction in Humans (1997)

Ang II markedly enhances sympathetic influences on coronary circulation in humans, presumably by acting at the arteriolar level. This may explain the blunting effect of ACE inhibition on sympathetic coronary vasoconstriction in patients with coronary artery disease.
A new consistency protocol implemented in the CAliF system (2002)

We propose a new consistency protocol for distributed shared memory (DSM) where different shared objects are replicated at each site. This protocol was developed for the cooperative platform called CAliF: Cooperative Application Framework. This system uses DSM to transparently handle the data sharing. We present an algorithm which uses the token technique. Updates of shared data are carried through a virtual ring on the token, named Pilgrim. The Pilgrim protocol provides both reliable consistency and guaranteed performance according to the type of application described. The protocol is described, proved and then simulated using the SPIN model checker and we demonstrate its qualities.
Light Reflectance Spectroscopy to Detect Positive Surgical Margins on Prostate Cancer Specimens (2015)

Light reflectance spectroscopy can identify positive surgical margins accurately in fresh ex vivo radical prostatectomy specimens. Further study is required to determine whether such analysis may be used in real time to improve surgical decision making and decrease positive surgical margin rates.
A research on combination methods for ensembles of multilayer feedforward (2006)

As shown in the bibliography, training an ensemble of networks is an interesting way to improve the performance with respect to a single network. The two key factors to design an ensemble are how to train the individual networks and how to combine the different outputs of the networks to give a single output class. In this paper, we focus on the combination methods. We study the performance of fourteen different combination methods for ensembles of the type "simple ensemble" and "decorrelated". In the case of the "simple ensemble" and low number of networks in the ensemble, the method Zimmermann gets the best performance. When the number of networks is in the range of 9 and 20 the weighted average is the best alternative. Finally, in the case of the ensemble "decorrelated" the best performing method is averaging over a wide spectrum of the number of networks in the ensemble.
RNA circularization strategies in vivo and in vitro (2015)

In the plenitude of naturally occurring RNAs, circular RNAs (circRNAs) and their biological role were underestimated for years. However, circRNAs are ubiquitous in all domains of life, including eukaryotes, archaea, bacteria and viruses, where they can fulfill diverse biological functions. Some of those functions, as for example playing a role in the life cycle of viral and viroid genomes or in the maturation of tRNA genes, have been elucidated; other putative functions still remain elusive. Due to the resistance to exonucleases, circRNAs are promising tools for in vivo application as aptamers, trans-cleaving ribozymes or siRNAs. How are circRNAs generated in vivo and what approaches do exist to produce ring-shaped RNAs in vitro? In this review we illustrate the occurrence and mechanisms of RNA circularization in vivo, survey methods for the generation of circRNA in vitro and provide appropriate protocols.
Antibacterial Activity of Retinaldehyde against <i>Propionibacterium acnes</i> (1999)

The MIC of retinaldehyde against P. acnes suggests a direct antibacterial activity. Daily topical application of 0.05% retinaldehyde is associated with a clear reduction of the P. acnes density.
Sequence Comparison of Yeast ATP-binding Cassette Proteins (1995)

A critical aspect of cellular physiology is the selective transport of ions, nutrients, proteins, and signaling molecules across cellular and organellar membranes, processes that are mediated by specific transporter and channel proteins. Over the past decade, molecular characterization has revealed that these transmembrane proteins can be grouped into discrete superfamilies. Members of a particular superfamily are similar in sequence, overall structure, and, presumably, in their mechanism of action. The largest of these groups, and the most intensively studied in recent years, is the ATP-binding cassette (ABC) superfamily, also called the "traffic ATPases," which presently comprises more than 100 members and continues to grow at a rapid rate (Higgins 1992; Doige and Ames 1993). ABC proteins can be found in both prokaryotes and eukaryotes and are present not only in the plasma membrane but also in intracellular organellar membranes.
A1 adenosine receptor antagonists block ischemia-reperfusion injury of the heart. (1996)

A1 adenosine receptor antagonists significantly reduce ischemia-reperfusion injury of the heart. A1 adenosine receptor antagonists may be useful for the prevention or early treatment of ischemia-reperfusion injury of the heart after coronary artery bypass graft surgery or cardiac transplant surgery and during or after angioplasty or thrombolytic therapy of the heart.
Follicular Depletion During the Menopausal Transition: Evidence for Accelerated Loss and Ultimate Exhaustion* (1987)

Although the menopause is generally considered to be the consequence of follicular exhaustion, the relationship between follicle number and the menopausal transition has not been explicity studied. We addressed this question in 17 women, aged 45-55 yr, who were undergoing elective total abdominal hysterectomy and salpingo-oophorectomy. The women were divided into 3 groups according to their menstrual history: 1) menstruating regularly (n = 6), 2) perimenopausal (irregular menses; n = 7), and 3) postmenopausal (greater than 1 yr since last menses; n = 4). The mean ages of the 3 groups were similar. Menstrual histories were confirmed by plasma hormone levels and endometrial histology. One ovary from each woman was serially sectioned for determination of follicle numbers. The mean number of primordial follicles in the ovaries of women who were still menstruating regularly was 10-fold higher than that in perimenopausal women [1392 +/- 355 (+/- SEM) vs. 142 +/- 72]. Follicles were virtually absent in the postmenopausal ovaries. Comparison of these data with those obtained by others in younger women suggests that follicular depletion accelerates dramatically in the last decade of menstrual life. These results support the view that declining follicular reserve is the immediate cause of both the perimenopausal and menopausal transitions, and indicate that the rate and, therefore, the regulation of follicular depletion change during the final phase of reproductive life.
Channel reassignment algorithm in multiple carrier hopping TDMA systems (1993)

Channel reassignment schemes used in multiple carrier hopping time-division multiple access (MCH-TDMA) systems are described. In MCH-TDMA systems channels are identified by two degrees of freedom: carrier frequency and time slot. The overlap-chain concept in which related calls from the same transmitting station to the same receiving station are grouped into contiguous streams is introduced. Using this concept, one channel can always be assigned to a call blocked due to inefficient assignment by reassigning channels to calls in progress within two or three time slots. A channel reassignment algorithm called OVERLAP-CHAINING which provides efficient means to reassign channels to calls in progress is proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Vanadium Oxide Films Synthesized by CVD and Used as Positive Electrodes in Secondary Lithium Batteries (2004)

Vanadium oxide films were synthesized by chemical vapor deposition from pure or diluted precursor. An annealing process at 500°C was required to obtain crystallized X-ray diffraction patterns have pointed out the influence of the operating conditions for the vanadium oxide deposition on the crystallites sizes. No significant difference in the roughness factor was observed by atomic force microscopy measurements before and after annealing at 500°C. As-deposited films were also directly obtained by changing the operating conditions. The insertion/deinsertion of into the host structure was investigated in 1 M -propylene carbonate. films exhibit low irreversible capacity and high cyclability even for a deep lithium insertion ratio; in addition, only small amounts of γ-phases were formed during cycle life at low potential without significant effects on its electrochemical performance. After subsequent cycles between 3.8 and 2.2 V vs. the reversible capacity is found to be ≈250 mAh g−1 close to the theoretical one. films exhibit reversible capacity of about 410 mAh g−1 © 2004 The Electrochemical Society. All rights reserved.
Resisting structural re-identification in anonymized social networks (2008)

We identify privacy risks associated with releasing network data sets and provide an algorithm that mitigates those risks. A network consists of entities connected by links representing relations such as friendship, communication, or shared activity. Maintaining privacy when publishing networked data is uniquely challenging because an individual's network context can be used to identify them even if other identifying information is removed. In this paper, we quantify the privacy risks associated with three classes of attacks on the privacy of individuals in networks, based on the knowledge used by the adversary. We show that the risks of these attacks vary greatly based on network structure and size. We propose a novel approach to anonymizing network data that models aggregate network structure and then allows samples to be drawn from that model. The approach guarantees anonymity for network entities while preserving the ability to estimate a wide variety of network measures with relatively little bias.
ChemInform Abstract: Electrophilic Substitution in Indoles. Part 16. The Formation of Indolobenzothiazines and Indolobenzothiazepines by Intramolecular Cyclization of (o‐Nitrophenylthio)indoles. (1989)

Abstract Deoxygenation of various (o‐nitrophenylthio)indoles such as (I), (V) or (VIII) affords a variety of cyclized products such as the spiro‐oxindole (III), the indolobenzothiazines (IV) or (IX) and the indolobenzothiazepine (VI).
Treatment of urban stormwater for dissolved pollutants: A comparative study of natural organic filter media (2005)

Sorption capacities were evaluated for the dissolved stormwater (SW) pollutants onto two tree mulches and jute fiber. SW spiked with predetermined concentrations of copper (Cu), cadmium (Cd), hexavalent chromium (Cr +6), lead (Pb), zinc (Zn), and benzo[a]pyrene (B[a]P), naphthalene (NP), fluoranthene (FA), 1,3-dichlorobenzene (DCB), and butylbenzylphthalate (BBP) were used in this study. Each medium removed close to 100 percent of all the pollutants at the concentrations studied. Sorption capacities (μg/g) of the three organic media were in the order of jute > hardwood mulch > softwood mulch, and on a mole basis, both the heavy metals and the toxic organics were sorbed by the three media in an identical sequence: Cr +6 > Cu, Zn > Cd > Pb; and NP > DCB > FA > B[a]P > BBP. Sorption capacities of the hardwood wood mulch and jute fiber for the pollutants were correlated with distinctive physical properties of the pollutants. © 2005 Wiley Periodicals, Inc.
Contribution of the tetrodotoxin-resistant voltage-gated sodium channel Na V 1.9 to sensory transmission and nociceptive behavior (2005)

The transmission of pain signals after injury or inflammation depends in part on increased excitability of primary sensory neurons. Nociceptive neurons express multiple subtypes of voltage-gated sodium channels (NaV1s), each of which possesses unique features that may influence primary afferent excitability. Here, we examined the contribution of NaV1.9 to nociceptive signaling by studying the electrophysiological and behavioral phenotypes of mice with a disruption of the SCN11A gene, which encodes NaV1.9. Our results confirm that NaV1.9 underlies the persistent tetrodotoxin-resistant current in small-diameter dorsal root ganglion neurons but suggest that this current contributes little to mechanical thermal responsiveness in the absence of injury or to mechanical hypersensitivity after nerve injury or inflammation. However, the expression of NaV1.9 contributes to the persistent thermal hypersensitivity and spontaneous pain behavior after peripheral inflammation. These results suggest that inflammatory mediators modify the function of NaV1.9 to maintain inflammation-induced hyperalgesia.
IntraLase Femtosecond Laser vs Mechanical Microkeratomes in LASIK for Myopia: A Systematic Review and Meta-analysis (2012)

According to the available data, LASIK with the IntraLase femtosecond laser offers no significant benefits over LASIK with microkeratomes in regards to safety and efficacy, but has potential advantages in predictability.
Eukaryotic DNA Polymerases: Proposal for a Revised Nomenclature (2001)

Pol polymeraseIn 1975, a Greek letter nomenclature system was introduced to designate DNA polymerases from mammalian cells (1). Ten years ago, progress in the biochemical analysis of eukaryotic DNA polymerases and in the isolation of their genes, particularly in the yeast Saccharomyces cerevisiae, necessitated a revision of the Greek letter nomenclature system and an expansion to include all eukaryotic organisms (2). Until a few years ago, this system sufficed to designate the six known DNA polymerases α, β, γ, δ, ε, and ζ.
Red Cell Cytograms Generated by an ADVIA 120 Automated Hematology Analyzer: Characteristic Patterns in Common Hematological Conditions (2009)

BackgroundGraphical data output from automated hematology analyzers, especially those related to red blood cells, have been traditionally ignored in favor of the more frequently used numerical values. This study presents characteristic red cell cytograms generated by Advia-120, a 5-part automated hematology analyzer, as seen in common hematological conditions.
Primary structure of endoglin, an RGD-containing glycoprotein of human endothelial cells. (1990)

Endoglin is a major glycoprotein of human vascular endothelium. As observed with monoclonal antibody 44G4, the distribution of endoglin is restricted to endothelial cells in all tissues except bone marrow. cDNA clones were isolated from an endothelial cell lambda gt11 cDNA library using a rabbit antibody prepared against endoglin purified from placenta. Eleven antibody-positive and cross-hybridizing clones were obtained; reactivity with endothelial cell 3.4-kilobase mRNA transcript was observed. The N-terminal sequence of placental endoglin was determined and found within the deduced protein sequence, thus confirming the identity of the cDNA and revealing a partial signal peptide. Endoglin is a type I integral membrane protein of Mr = 68,051 with an extracellular region of 561 amino acids, a hydrophobic transmembrane domain, and a 47-residue cytoplasmic tail. There are four potential N-linked glycosylation sites in the N-terminal domain and a probable O-glycan domain rich in Ser and Thr residues proximal to the membrane-spanning domain. Data base searches revealed that endoglin is a novel protein. The sequence contains an RGD tripeptide (374-376), the first identified on a surface protein of endothelium. The presence of RGD, a key recognition structure in cellular adhesion, suggests a critical role for endoglin in the binding of endothelial cells to integrins and/or other RGD receptors.