gebhart/patrepeval huggingface dataset:
546 km, 140 Mbit/s FSK coherent transmission experiment through 10 cascaded semiconductor laser amplifiers (1989)

The effect of the spontaneous emission noise on coherent systems in a multistage semiconductor laser amplifier repeater system is experimentally examined. By appropriate adjustment of the input power level to each amplifier, 546 km FSK transmission at 140 Mbit/s using 10 cascaded amplifiers is demonstrated without power penalty.
Continuous culture selection of bifidobacteria and lactobacilli from human faecal samples using fructooligosaccharide as selective substrate (1998)

The human large intestine contains a large and diverse population of bacteria. Certain genera, namely Bifidobacterium and Lactobacillus, are thought to exert health-promoting effects. Prebiotics such as fructooligosaccharides (FOS) have been shown to stimulate the growth of endogenous bifidobacteria. In this study, changes of lactic acid producing bacteria in continuous culture fermentors (semi-defined, anaerobic medium containing 5 g 1(-1) FOS, dilution rate of 0.1 h-1, pH 5.5) were followed over a 21 d period after inoculation with blended human faeces from four healthy adults. Samples were also taken every 3 d for influent/effluent FOS, short chain fatty acid (SCFA), lactate and microbiological analyses. Results showed that SCFA concentrations decreased abruptly 1 d after inoculation while lactate concentrations increased. Classical methods of enumeration using selective media showed that the proportion of total culturable count represented by bifidobacteria and lactobacilli increased from 11.9% on day 1 to 98.1% on day 21. However, molecular methods using genus-specific 16S rRNA oligonucleotide probes indicated that the bifidobacterial population maintained a level between 10 and 20% of total 16S rRNA during the first 6 d and disappeared rapidly when the maximum concentration of lactate was reached. Lactobacilli, which were initially present in low numbers, increased until day 9 and remained at high levels (20-42% of total 16S rRNA) to day 21, with the exception of day 18. Although FOS has usually been regarded as a selective substrate for bifidobacteria, these observations suggest that: (1) lactobacilli are also able to use FOS, (2) lactobacilli can out-compete bifidobacteria in continuous culture at pH 5.2-5.4 when FOS is the primary carbon and energy source, and (3) bifidobacteria can grow faster on FOS than lactobacilli under controlled conditions.
Substructure solution withSHELXD (2002)

Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0-3.5 A, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package.
Identifying groups of interest through temporal analysis and event response monitoring (2013)

We present a method for finding groups of interest in large social networks. A temporal group detection algorithm identifies tightly connected groups by analyzing communications as they unfold over time. Since the number of groups found through temporal group detection may be too large to allow for manual analysis of their behavior, we also present an algorithm to identify groups of interest within an existing set of groups. This algorithm works by observing how groups react to key events and finds groups of interest by noting which groups respond anomalously. We demonstrate this approach on two social media datasets collected from Twitter. The first dataset involves tweets from Afghanistan when Afghanistan signed a letter of cooperation with India. The second dataset involves tweets surrounding the death of Steve Jobs. In both cases, our algorithm was able to identify appropriate groups.
Solving the Distal Reward Problem through Linkage of STDP and Dopamine Signaling (2007)

In Pavlovian and instrumental conditioning, reward typically comes seconds after reward-triggering actions, creating an explanatory conundrum known as "distal reward problem": How does the brain know what firing patterns of what neurons are responsible for the reward if 1) the patterns are no longer there when the reward arrives and 2) all neurons and synapses are active during the waiting period to the reward? Here, we show how the conundrum is resolved by a model network of cortical spiking neurons with spike-timing-dependent plasticity (STDP) modulated by dopamine (DA). Although STDP is triggered by nearly coincident firing patterns on a millisecond timescale, slow kinetics of subsequent synaptic plasticity is sensitive to changes in the extracellular DA concentration during the critical period of a few seconds. Random firings during the waiting period to the reward do not affect STDP and hence make the network insensitive to the ongoing activity-the key feature that distinguishes our approach from previous theoretical studies, which implicitly assume that the network be quiet during the waiting period or that the patterns be preserved until the reward arrives. This study emphasizes the importance of precise firing patterns in brain dynamics and suggests how a global diffusive reinforcement signal in the form of extracellular DA can selectively influence the right synapses at the right time.
Finding statistics online: how to locate the elusive numbers you need (1998)

Quick start Statistics basics The sources General search tips Finding demographics Finding industry, market, & general business statistics Finding health & medical statistics Finding historical statistics Finding public opinion & trend statistics Finding political statistics Finding sports statistics Finding technology statistics Finding education statistics Finding transportation statistics
Pulmonary Veins‐Left Atrial Junction: Anatomic and Histological Study (2000)

Pulmonary veins (PVs) are the target of ablation procedures to cure paroxysmal atrial fibrillation (PAF). There are few anatomic and histological studies of PVs. Sixteen human hearts were obtained from autopsies performed at our hospital and cadavers from a local medical school. The anatomic relationship between the PVs and the left atrium (LA) was categorized according to the spatial orientation of the veins within horizontal and vertical planes viewed from the dorsal aspect of the LA. The PVs were sectioned longitudinally, and the sections were stained with hematoxylin and eosin. In addition, selected sections were stained with antismooth muscle antibodies (vessel wall), antipankeratin, and antimyoglobin antibodies (myocardium). The PV-LA junction has variable orientations. Confluent superior and inferior veins, observed in 25% of the hearts, were more common on the left side. A myocardial sleeve extended from the LA onto the adventitial surface of the PV. The sleeve was distinct from the smooth muscle in the PV media, from which it was separated by loose fibrous strands. There was no microscopical boundary between the PV and the LA endocardium. The PV join the LA at variable angles. Each PV is surrounded by a myocardial sleeve extending from the LA.
OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding (2010)

Antibodies are an important class of proteins with many biomedical and biotechnical applications. Although there are a plethora of experimental techniques geared toward their efficient production, there is a paucity of computational methods for their de novo design. OptCDR is a general computational method to design the binding portions of antibodies to have high specificity and affinity against any targeted epitope of an antigen. First, combinations of canonical structures for the antibody complementarity determining regions (CDRs) that are most likely to be able to favorably bind the antigen are selected. This is followed by the simultaneous refinement of the CDR structures' backbones and optimal amino acid selection for each position. OptCDR is applied to three computational test cases: a peptide from the capsid of hepatitis C, the hapten fluorescein and the protein vascular endothelial growth factor. The results demonstrate that OptCDR can efficiently generate diverse antibody libraries of a pre-specified size with promising antigen affinity potential as exemplified by computationally derived binding metrics.
Bacterial DNA Containing CpG Motifs Stimulates Lymphocyte-Dependent Protection of Mice Against Lethal Infection with Intracellular Bacteria (1999)

Bacterial DNA containing unmethylated CpG motifs activates mammalian lymphocytes and macrophages to produce cytokines and polyclonal Ig. These include IFN-gamma, IL-12, TNF-alpha, and IL-6, which are important in the control of intracellular bacterial infection. Here, we show that bacterial DNA, as well as synthetic oligonucleotides containing CpG motifs, induce protection against large lethal doses of Francisella tularensis live vaccine strain (LVS) and Listeria monocytogenes. Methylation of DNA at CpG dinucleotides or inversion of the motif abolished this protection. Surprisingly, DNA-mediated protection was highly dependent on lymphocytes, particularly B cells, as well as the production of IFN-gamma. Optimal protection was elicited 2-3 days after inoculation with DNA and persisted for up to 2 wk. Further, animals surviving lethal challenge developed pathogen-specific secondary immunity. These findings indicate that host innate immune responses to bacterial DNA may contribute to the induction of protective immunity to bacteria and the subsequent development of memory.
Tandem Repeated Sequences within the Terminal Region of the Fowlpox Virus Genome (1989)

A 6.2 kb BamHI terminal fragment from fowlpox virus has been cloned and the nucleotide sequence was determined. The fragment was cloned by S1 digestion of viral DNA and therefore does not contain the covalently closed terminal loop. The cloned sequences comprise a short (230 bp) unique region at the terminal end, which is adjacent to a 3.87 bp long, AT-rich region consisting of sets of short tandemly repeated units, 32 and 56 bp long. The remainder of the fragment is composed of a 2.18 kb unique region containing three major open reading frames. The amino acid sequence encoded by one of these has some similarity to that of platelet-derived growth factor.
ChemInform Abstract: Activity and Reduction Behavior of Fused Iron Catalysts Containing Cobalt for Ammonia Synthesis: A Structure Study. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Angiographic Anatomy of the Coronary Sinus and Its Tributaries (1998)

Angiographic analysis of dimensions, tortuosity, number, and angulation of venous tributaries of the CS seems to allow the insertion of commercially available pacing leads in approximately 85% of cases. An increase in this percentage hinges on the development of new, dedicated leads.
Pure, postmitotic, polarized human neurons derived from NTera 2 cells provide a system for expressing exogenous proteins in terminally differentiated neurons (1992)

NTera 2/cl.D1 (NT2) cells, a human teratocarcinoma cell line, were manipulated following retinoic acid treatment to yield greater than 95% pure cultures of neuronal cells (NT2-N cells). The commitment of NT2-N cells to a stable neuronal phenotype is irreversible as judged by the lack of mitotic activity or phenotypic reversion over a period of 2 months in culture. Furthermore, NT2-N cells express a variety of neuronal markers including many neuronal cytoskeletal proteins, secretory markers, and surface markers. NT2-N cells resemble primary neuronal cultures from rodents morphologically and in density of process outgrowth and, like primary neurons, go on to elaborate processes that differentiate into axons and dendrites. This culture method yields sufficient highly differentiated postmitotic NT2-N cells for both biochemical and molecular biological studies. Indeed, when undifferentiated NT2 cells were stably transfected with a beta-galactosidase (beta-gal) expression plasmid, beta-gal expression was shown to be present in both undifferentiated NT2 and postmitotic NT2-N cells. Thus, the ability to transfect expression plasmids into undifferentiated NT2 cells will allow the introduction of normal and mutant gene products into cells that can then be induced to become stable, postmitotic human neurons. We conclude that NT2 cells and NT2-N cells represent a unique model system for studies of human neurons, and a novel vehicle for the expression of diverse gene products in terminally differentiated polarized neurons.
Maternal Antibodies: Clinical Significance, Mechanism of Interference with Immune Responses, and Possible Vaccination Strategies (2014)

Neonates have an immature immune system, which cannot adequately protect against infectious diseases. Early in life, immune protection is accomplished by maternal antibodies transferred from mother to offspring. However, decaying maternal antibodies inhibit vaccination as is exemplified by the inhibition of seroconversion after measles vaccination. This phenomenon has been described in both human and veterinary medicine and is independent of the type of vaccine being used. This review will discuss the use of animal models for vaccine research. I will review clinical solutions for inhibition of vaccination by maternal antibodies, and the testing and development of potentially effective vaccines. These are based on new mechanistic insight about the inhibitory mechanism of maternal antibodies. Maternal antibodies inhibit the generation of antibodies whereas the T cell response is usually unaffected. B cell inhibition is mediated through a cross-link between B cell receptor (BCR) with the Fcγ-receptor IIB by a vaccine-antibody complex. In animal experiments, this inhibition can be partially overcome by injection of a vaccine-specific monoclonal IgM antibody. IgM stimulates the B cell directly through cross-linking the BCR via complement protein C3d and antigen to the complement receptor 2 (CR2) signaling complex. In addition, it was shown that interferon alpha binds to the CD21 chain of CR2 as well as the interferon receptor and that this dual receptor usage drives B cell responses in the presence of maternal antibodies. In lieu of immunizing the infant, the concept of maternal immunization as a strategy to protect neonates has been proposed. This approach would still not solve the question of how to immunize in the presence of maternal antibodies but would defer the time of infection to an age where infection might not have such a detrimental outcome as in neonates. I will review successful examples and potential challenges of implementing this concept.
Recognition of multiple epitopes in the human melanoma antigen gp100 by tumor-infiltrating T lymphocytes associated with in vivo tumor regression. (1995)

Four of ten HLA-A2-restricted melanoma specific CTL that were derived from tumor-infiltrating lymphocytes (TIL) and administered to patients recognized the gp100 melanoma Ag and nine of ten recognized the MART-1 Ag. Adoptive transfer of the four gp100-reactive CTL, but not the other TIL, resulted in tumor regression when infused into autologous patients along with IL-2. Tumor regression was thus correlated with the recognition of gp100 by the administered T cells (p = 0.0048). To identify the epitopes recognized by these four gp100-reactive CTL, 169 peptides containing HLA-A2.1 binding motifs were synthesized and screened for their recognition by TIL using cytotoxicity and IFN-gamma release assays. Five gp100 epitopes (two for TIL620, three for TIL660, one for TIL1143, and two for TIL1200) were recognized by CTL derived from different patients. Five of eight HLA-A2 binding melanoma epitopes (five gp100, one MART-1/Melan-A, two tyrosinase) had intermediate binding affinity to HLA-A2.1. These gp100 epitopes may be responsible for mediating tumor rejection in vivo and thus may be useful for the development of immunotherapies for patients with melanoma.
Development of a Biorelevant, Material-Sparing Membrane Flux Test for Rapid Screening of Bioavailability-Enhancing Drug Product Formulations (2017)

Bioavailability-enhancing formulations are often used to overcome challenges of poor gastrointestinal solubility for drug substances developed for oral administration. Conventional in vitro dissolution tests often do not properly compare such formulations due to the many different drug species that may exist in solution. To overcome these limitations, we have designed a practical in vitro membrane flux test, that requires minimal active pharmaceutical ingredient (API) and is capable of rapidly screening many drug product intermediates. This test can be used to quickly compare performance of bioavailability-enhancing formulations with fundamental knowledge of the rate-limiting step(s) to membrane flux. Using this system, we demonstrate that the flux of amorphous itraconazole (logD = 5.7) is limited by aqueous boundary layer (ABL) diffusion and can be increased by adding drug-solubilizing micelles or drug-rich colloids. Conversely, the flux of crystalline ketoconazole at pH 5 (logD = 2.2) is membrane-limited, and adding solubilizing micelles does not increase flux. Under certain circumstances, the flux of ketoconazole may also be limited by dissolution rate. These cases highlight how a well-designed in vitro assay can provide critical insight for oral formulation development. Knowing whether flux is limited by membrane diffusion, ABL diffusion, or dissolution rate can help drive formulation development decisions. It may also be useful in predicting in vivo performance, dose linearity, food effects, and regional-dependent flux along the length of the gastrointestinal tract.
Si and GaAs photocapacitive MIS infrared detectors (1980)

Improvement of the previously reported photocapacitive MIS infrared detectors has led to the development of exceptional room-temperature devices. Unoptimized peak detectivities on the order of 1013 W−1 cm Hz1/2, a value which exceeds the best obtainable from existing solid-state detectors, have now been consistently obtained in Si and GaAs devices using high-capacitance LaF3 or composite LaF3/native-oxide insulating layers. The measured spectral response of representative samples is presented and discussed in detail together with a simple theory which accounts for the observed behavior. The response of an ideal MIS photocapacitor is also contrasted with that of both a conventional photoconductor and a p-i-n photodiode, and reasons for the superior performance of our detectors are given. Finally, fundamental studies on the electrical, optical, and noise characteristics of our MIS structures are analyzed and discussed in the context of infrared-detector applications.
Sex determination in the germ line of Drosophila depends on genetic signals and inductive somatic factors* (1989)

We have analyzed the mechanism of sex determination in the germ line of Drosophila by manipulating three parameters: (1) the ratio of X-chromosomes to sets of autosomes (X:A); (2) the state of activity of the gene Sex-lethal (Sxl), and (3) the sex of the gonadal soma. To this end, animals with a ratio of 2X:2A and 2X:3A were sexually transformed into pseudomales by mutations at the sex-determining genes Sxl (Sex-lethal), tra (transformer), tra-2 (transformer-2), or dsx (double-sex). Animals with the karyotype 2X;3A were also transformed into pseudofemales by the constitutive mutation SxlM1. The sexual phenotype of the gonads and of the germ cells was assessed by phase-contrast microscopy. Confirming the conclusions of Steinmann-Zwicky et al. (Cell 57, 157, 1989), we found that all three parameters affect sex determination in germ cells. In contrast to the soma in which sex determination is completely cell-autonomous, sex determination in the germ line has a non-autonomous component inasmuch as the sex of the soma can influence the sexual pathway of the germ cells. Somatic induction has a clear effect on 2X;2A germ cells that carry a Sxl+ allele. These cells, which form eggs in an ovary, can enter spermatogenesis in testes. Mutations that cause partial loss of function or gain of function of Sxl thwart somatic induction and, independently of the sex of the soma, dictate spermatogenesis or oogenesis, respectively. Somatic induction has a much weaker effect on 2X;3A germ cells. This ratio is essentially a male signal for germ cells which consistently enter spermatogenesis in testes, even when they carry SxlM1. In a female soma, however, SxlM1 enables the 2X;3A germ cells to form almost normal eggs. Our results show that sex determination in the germ line is more complex than in the soma. They provide further evidence that the state of Sxl, the key gene for sex determination and dosage compensation in the soma, also determines the sex of the germ cells, and that, in the germ line, the state of activity of Sxl is regulated not only by the X:A ratio, but also by somatic inductive stimuli.
X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. (1990)

The structure of a crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site has been determined. The sequence of the inhibitor JG-365 is Ac-Ser-Leu-Asn-Phe-psi[CH(OH)CH2N]-Pro-Ile-Val-OMe; the Ki is 0.24 nM. The hydroxyethylamine moiety, in place of the normal scissile bond of the substrate, is believed to mimic a tetrahedral reaction intermediate. The structure of the complex has been refined to an R factor of 0.146 at 2.4-A resolution by using restrained least squares with rms deviations in bond lengths of 0.02 A and bond angles of 4. The bound inhibitor diastereomer has the S configuration at the hydroxyethylamine chiral carbon, and the hydroxyl group is positioned between the active site aspartate carboxyl groups within hydrogen bonding distance. Comparison of this structure with a reduced peptide bond inhibitor-protease complex indicates that these contacts confer the exceptional binding strength of JG-365.
Clarifications to the DNS Specification (1997)

This document considers some areas that have been identified as problems with the specification of the Domain Name System, and proposes remedies for the defects identified. Eight separate issues are considered: