gebhart/patrepeval huggingface dataset:
Order selection for AR models by predictive least squares (1988)

A criterion is presented for selecting the order of autoregressive models that, unlike the existing criteria, is amenable to online or adaptive operation. It is based on the predictive least squares (PLS) principle and is implemented in a computationally efficient way by predictive lattice filters. The consistency of the criterion is proved, and its performance is demonstrated by computer simulations. Assuming the data to be generated by an AR model of order p, the order selection criterion should select the correct order p with probability that converges to 1 as the sample size grows to infinity. It is proved that the PLS criterion is indeed consistent, thereby giving a solid justification for the criterion. Simulation results that demonstrate the performance of the PLS criterion in comparison to H. Akaike's AIC (1973) and the MDL criteria of J. Rissanen (1978) and G. Schwarz (1978) are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Error Control in Duobinary Data Systems by Means of Null Zone Detection (1968)

It is shown that duobinary data system performance can be improved at least 0.7 dB in the presence of Gaussian noise by using a null zone detection procedure. Most nulls can be replaced by correct values using the analog signal redundancy information. Nulls which cannot be replaced using the analog redundancy are restored to their most probable values on the basis of the received sample levels.
Albedo Concentration in the Anterior Eye: A Phenomenon that Locates Some Solar Diseases (1990)

I describe concentrations of reflected solar radiation (albedo) found at the usual sites of various conditions associated with exposure to the sun--pterygium, pinguecula, climatic droplet keratopathy and cataract and eyelid malignancy. Since the degree of limbal albedo concentration appears to be related to corneal curvature, patients at risk can be identified by a simple test and preventative measures taken.
Placebo-controlled trials: good science or medical neglect? (2000)

The placebo-controlled clinical trial has a long history of being the standard for clinical investigations of new drugs. By blindly and randomly allocating similar patients to a control group that receives a placebo and an experimental group, investigators can ensure that any possible placebo effect will be minimized in the final statistical analysis. Although this approach to clinical research is scientifically sound, ethical concerns arise in some cases that outweigh the benefits of this protocol design. Even though patients may be advised of the likelihood of being placed in a placebo group and that the intent of the clinical trial is research, not medical care, they often hope for some level of treatment. More importantly, when effective treatments exist, research participants who have progressive, burdensome disease should be given standard treatment as the control agent.

Using a recent example of a clinical trial of a new drug for treating rheumatoid arthritis, we argue that research participants who have burdensome, progressive disease should not be exposed to the risks of placebo-controlled trials. Historical controls and active controls may need more people in a particular trial but do not deprive patients of approved treatment. We propose several guidelines for considering the ethical use of placebo controls in clinical trials and call on research regulatory agencies to standardize their recommendations.

Summary points




The use of placebo controls in clinical research that involves patients who have an active disease for which there is approved treatment is ethically questionable and may represent substandard care


The use of active or historical controls in clinical research may address these ethical questions


Federal guidelines say that a condition of clinical equipoise should exist before a placebo-control study is started. Although this is a reasonable guideline, sponsors or investigators may be ignoring it


Research participants with active disease are likely to believe they will possibly benefit from taking part in trials. This therapeutic misconception may not be obviated by an informed consent form
Improving the Clostridium acetobutylicum butanol fermentation by engineering the strain for co-production of riboflavin (2010)

Solvent-producing clostridia are well known for their capacity to use a wide variety of renewable biomass and agricultural waste materials for biobutanol production. To investigate the possibility of co-production of a high value chemical during biobutanol production, the Clostridium acetobutylicum riboflavin operon ribGBAH was over-expressed in C. acetobutylicum on Escherichia coli-Clostridium shuttle vector pJIR750. Constructs that either maintained the original C. acetobutylicum translational start codon or modified the start codons of ribG and ribB from TTG to ATG were designed. Riboflavin was successfully produced in both E. coli and C. acetobutylicum using these plasmids, and riboflavin could accumulate up to 27 mg/l in Clostridium culture. Furthermore, the C. acetobutylicum purine pathway was modified by over-expression of the Clostridium purF gene, which encodes the enzyme PRPP amidotransferase. The function of the plasmid pJaF bearing C. acetobutylicum purF was verified by its ability to complement an E. coli purF mutation. However, co-production of riboflavin with biobutanol by use of the purF over-expression plasmid was not improved under the experimental conditions examined. Further rational mutation of the purF gene was conducted by replacement of amino acid codons D302 V and K325Q to make it similar to the feedback-resistant enzymes of other species. However, the co-expression of ribGBAH and purFC in C. acetobutylicum also did not improve riboflavin production. By buffering the culture pH, C. acetobutylicum ATCC 824(pJpGN) could accumulate more than 70 mg/l riboflavin while producing 190 mM butanol in static cultures. Riboflavin production was shown to exert no effect on solvent production at these levels.
The Effects of Poloxamer-188 on Left Ventricular Function in Chronic Heart Failure After Myocardial Infarction (2012)

Treatment with P-188 improves the LV function and partially reverses maladaptive LV remodeling in rats with moderate CHF after MI. These data introduce the idea of using a biological membrane sealant as a new approach to treating CHF after MI.
COMPUTERS CAN NOW PERFORM VITAL FUNCTIONS SAFELY (1979)

Early attempts to apply data processors to tasks previously reserved for vital relays concentrated on redundancy and voting systems as protection against hardware failure. When logic performed by fail-safe relays, with predictable failure modes, is replaced by computers with unpredictable failure modes, several factors must be considered. Not enough attention was devoted to software with the computers and no complex program can be considered foolproof even after a lengthy period in service. L. M. Ericsson utilizes parallel running of non-identical programs with multi-stage comparison to guard against failures. This technique has been applied to large interlockings and to on-train signaling and speed-control systems. Ahead is the possibility that the functions of logic and output checking may be carried out within a single microprocessor, using fault-tolerant programming.
A New Approach of E-beam Proximity Effect Correction for High-Resolution Applications (1998)

The e-beam proximity effect is well known as one of the limiting factors in e-beam lithography. As features get smaller the need for e-beam proximity effect correction (EPC) increases. There exist different approaches to cover these effects by varying dose or shape of the pattern layout during the exposure step. Both of these basic approaches have drawbacks limiting their application. For example, the EPC correction by shape variation underlies constraints such as neighbouring features, the exposure grid of the e-beam tool and writing time. EPC by dose variation fails in cases the feature size is very close to the process dependent forward scattering parameter alpha. To guarantee CD uniformity in these cases a negative dose assignment would be necessary, which is practically impossible. The paper presents a new correction scheme based on dose assignment and geometry variation at the same time. After a short introduction the theoretical description of the method is given. Dose and geometry modifications are calculated using a Fast Fourier Algorithm. Due to the ability of changing the geometry depending on feature size and feature neighbourhood even very small features can be printed correctly. This flexibility is the main advantage compared to already existing methods. Pattern fidelity and linearity can be improved drastically. Resolution limits can be pushed further down. The application of the automatic correction to high resolution features with a feature size of 100 nm are demonstrated. The CD linearity is investigated and demonstrated using a real device patterns.
Pathogenicity and growth characteristics of selected infectious laryngotracheitis virus strains from the United States (2009)

In a recent study, several US infectious laryngotracheitis virus (ILTV) strains and field isolates were genotyped by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) into nine different genotypes. All of the commercial poultry isolates were identified within genotypes IV, V, and VI. Based on the PCR-RFLP, Group IV isolates were characterized as genetically identical to the chicken embryo origin (CEO) vaccines, Group V as genetically closely related to the CEO vaccines, and Group VI as genetically different to the vaccine strains. The objective of this study was to determine the pathogenicity and growth characteristics of six ILTV commercial poultry isolates as compared with the CEO vaccine. Two isolates representative of PCR-RFLP Groups IV, V, and VI were selected. Differences in disease severity, viral tissue distribution in chickens, and plaque formation ability in cell culture were observed among viral genotypes IV, V, and VI, and between V-A and V-B isolates. Mild respiratory clinical signs were produced by IV-A, IV-B and the CEO vaccine, while VI-A and VI-B isolates produced severe respiratory signs and severe depression, and during the peak of clinical signs both isolates were re-isolated from the conjunctiva, sinus, trachea and thymus. Similarly to Group VI isolates, V-A and V-B produced severe respiratory signs, depression, and were re-isolated from conjunctiva, sinus, and trachea; on cell culture, both isolates produced significant larger plaques than any of the other isolates analysed. Overall, differences in pathogenicity and growth characteristics were observed among genetically closely related US ILTV isolates; however, complete genomes will be necessary to identify molecular determinants linked to the pathogenic viral phenotypes.
Insight into Invertebrate Defensin Mechanism of Action (2010)

Three oyster defensin variants (Cg-Defh1, Cg-Defh2, and Cg-Defm) were produced as recombinant peptides and characterized in terms of activities and mechanism of action. In agreement with their spectrum of activity almost specifically directed against Gram-positive bacteria, oyster defensins were shown here to be specific inhibitors of a bacterial biosynthesis pathway rather than mere membrane-active agents. Indeed, at lethal concentrations, the three defensins did not compromise Staphylococcus aureus membrane integrity but inhibited the cell wall biosynthesis as indicated by the accumulation of the UDP-N-acetylmuramyl-pentapeptide cell wall precursor. In addition, a combination of antagonization assays, thin layer chromatography, and surface plasmon resonance measurements showed that oyster defensins bind almost irreversibly to the lipid II peptidoglycan precursor, thereby inhibiting the cell wall biosynthesis. To our knowledge, this is the first detailed analysis of the mechanism of action of antibacterial defensins produced by invertebrates. Interestingly, the three defensins, which were chosen as representative of the oyster defensin molecular diversity, bound differentially to lipid II. This correlated with their differential antibacterial activities. From our experimental data and the analysis of oyster defensin sequence diversity, we propose that oyster defensin activity results from selective forces that have conserved residues involved in lipid II binding and diversified residues at the surface of oyster defensins that could improve electrostatic interactions with the bacterial membranes.
SH2 Domains Mediate the Sequential Phosphorylation of HS1 Protein by p72<i><sup>s</sup><sup>y</sup><sup>k</sup></i> and Src-Related Protein Tyrosine Kinases (1996)

The protein tyrosine kinase p72syk readily phosphorylates hematopoietic linkage cell-specific protein p50/HS1 with high stoichiometry (up to 4 mol of Pi/mol of protein) and favorable kinetic constants (Km 77 nM, kcat 0.37 s-1), at sites that display the motif that is specifically recognized by the HS2 domains of Src tyrosine kinases. Such a phosphorylation converts p50/HS1 into a good substrate for c-Fgr, which in contrast is nearly inactive on nonphosphorylated p50/HS1. A phosphopeptide reproducing one of the main p50/HS1 site affected by p72syk, but neither its dephosphorylated derivative nor other phosphopeptides with different structure, blocks the secondary phosphorylation of phospho(p50/HS1) by c-Fgr but not its primary phosphorylation by p72syk. It also prevents the coimmunoprecipitation of phospho(HS1) with c-Fgr by anti-(c-Fgr) antibodies. In contrast the HS1[393-402] phosphopeptide is ineffective on the kinase activity of c-Fgr when tested with peptide substrates, showing that inhibition of p50/HS1 phosphorylation is not exerted at the catalytic site of c-Fgr. The sequential phosphorylation of p50/HS1 as well as its specific blockage by the HS1 phosphopeptide is also observable if c-Fgr is replaced by two other Src-related kinases, namely, Lyn and Fyn, as secondary phosphorylating agents. None of these Src-related kinases, however, can carry out the phosphorylation of p50/HS1 at the sites affected by p72syk, even after prolonged incubation. Our data suggest that sequential phosphorylation might represent a general mechanism by which p72syk and other Syk-related kinases generate substrates for Src-related protein tyrosine kinases. They also show that sequential phosphorylation (requiring the concerted action of a primary and a secondary kinases) cannot be surrogated by "processive" phosphorylation where a single kinase catalyzes both the primary and secondary phosphorylation, although both these modes of multiple phosphorylation are based on interactions between SH2 domains of the kinases and phosphotyrosyl sites of the substrate.
Automated image analysis methods for 3‐D quantification of the neurovascular unit from multichannel confocal microscope images (2005)

Associative features across fluorescence channels, in combination with standard features, enable integrative structural and functional analysis of the NVU. By labeling additional structural and functional entities, this method can be scaled up to larger-scale systems biology studies that integrate spatial and molecular information.
A comparative study evaluating the tolerability and efficacy of two topical therapies for the treatment of keloids and hypertrophic scars. (2010)

Both OE and HSE were more effective than placebo in the management of hypertrophic scars and keloids.
Learning Low-Dimensional Representations of Medical Concepts. (2016)

We show how to learn low-dimensional representations (embeddings) of a wide range of concepts in medicine, including diseases (e.g., ICD9 codes), medications, procedures, and laboratory tests. We expect that these embeddings will be useful across medical informatics for tasks such as cohort selection and patient summarization. These embeddings are learned using a technique called neural language modeling from the natural language processing community. However, rather than learning the embeddings solely from text, we show how to learn the embeddings from claims data, which is widely available both to providers and to payers. We also show that with a simple algorithmic adjustment, it is possible to learn medical concept embeddings in a privacy preserving manner from co-occurrence counts derived from clinical narratives. Finally, we establish a methodological framework, arising from standard medical ontologies such as UMLS, NDF-RT, and CCS, to further investigate the embeddings and precisely characterize their quantitative properties.
The sugar phosphotransferase system of <i>Streptomyces coelicolor</i> is regulated by the GntR‐family regulator DasR and links <i>N</i>‐acetylglucosamine metabolism to the control of development (2006)

Members of the soil-dwelling, sporulating prokaryotic genus Streptomyces are indispensable for the recycling of the most abundant polysaccharides on earth (cellulose and chitin), and produce a wide range of antibiotics and industrial enzymes. How do these organisms sense the nutritional state of the environment, and what controls the signal for the switch to antibiotic production and morphological development? Here we show that high extracellular concentrations of N-acetylglucosamine, the monomer of chitin, prevent Streptomyces coelicolor progressing beyond the vegetative state, and that this effect is absent in a mutant defective of N-acetylglucosamine transport. We provide evidence that the signal is transmitted through the GntR-family regulator DasR, which controls the N-acetylglucosamine regulon, including the pts genes ptsH, ptsI and crr needed for uptake of N-acetylglucosamine. Deletion of dasR or the pts genes resulted in a bald phenotype. Binding of DasR to its target genes is abolished by glucosamine 6-phosphate, a central molecule in N-acetylglucosamine metabolism. Extracellular complementation experiments with many bld mutants showed that the dasR mutant is arrested at an early stage of the developmental programme, and does not fit in the previously described bld signalling cascade. Thus, for the first time we are able to directly link carbon (and nitrogen) metabolism to development, highlighting a novel type of metabolic regulator, which senses the nutritional state of the habitat, maintaining vegetative growth until changing circumstances trigger the switch to sporulation. Our work, and the model it suggests, provide new leads towards understanding how microorganisms time developmental commitment.
An implantable radiation dosimeter for use in external beam radiation therapy (2004)

An implantable radiation dosimeter for use with external beam therapy has been developed and tested both in vitro and in canines. The device uses a MOSFET dosimeter and is polled telemetrically every day during the course of therapy. The device is designed for permanent implantation and also acts as a radiographic fiducial marker. Ten dogs (companion animals) that presented with spontaneous, malignant tumors were enrolled in the study and received an implant in the tumor CTV. Three dogs received an additional implant in collateral normal tissue. Radiation therapy plans were created for the animals and they were treated with roughly 300 cGy daily fractions until completion of the prescribed cumulative dose. The primary endpoints of the study were to record any adverse events due to sensor placement and to monitor any movement away from the point of placement. No adverse events were recorded. Unacceptable device migration was experienced in two subjects and a retention mechanism was developed to prevent movement in the future. Daily dose readings were successfully acquired in all subjects. A rigorous in vitro calibration methodology has been developed to ensure that the implanted devices maintain an accuracy of +/-3.5% relative to an ionization chamber standard. The authors believe that an implantable radiation dosimeter is a practical and powerful tool that fosters individualized patient QA on a daily basis.
Long-term effects of non-linear frequency compression for children with moderate hearing loss (2011)

These results suggest that NLFC improves audibility for and recognition of high-frequency speech sounds for children with moderate to moderately-severe hearing loss. In many cases, improvements found with NLFC increased with a longer period of acclimatization to the technology.
Heroes of the Epidemic (1989)

Australia's AIDS stand has been generally good. But it's threatened by the 'roll back permissiveness' tide. Ken Davis looks ahead into the new decade, and sees the gay community still at the forefront.
Reduction of gray level disturbances in plasma display panels (2004)

An effective method to reduce gray level disturbances in plasma display panels (PDPs) is proposed in this work. First, we develop a systematic model for gray level disturbances, which occur when PDPs display moving image sequences. Then, we derive an ideal condition for the disturbances removal. Based on the condition, we propose the optimal subfield and driving vectors to minimize the disturbances. Simulation results show that the proposed algorithm provides a good moving image quality.
Fluorouracil and high-dose leucovorin in previously treated patients with metastatic breast cancer. (1989)

The efficacy and toxicity of leucovorin 500 mg/m2 administered intravenously (IV) over 30 minutes daily for five days followed in one hour by fluorouracil (5-FU) 375 mg/m2 administered IV daily for five days, each given every 3 weeks, was assessed in 54 previously treated patients with metastatic breast cancer. An overall objective response rate of 24% was achieved (95% confidence interval, 13% to 38%), with an additional 56% of patients maintaining stable disease. Eleven of 12 patients who responded had received previous 5-FU therapy. Toxicity of this regimen included grade 3 diarrhea in 13%, grade 3 or 4 mucositis in 33%, grade 3 or 4 granulocytopenia in 65%, and grade 3 or 4 thrombocytopenia in 19%. Delay of treatment was required for hematologic toxicity in 44 patients. Thirty-eight patients required dose reductions due to toxicity. Biochemical evaluation of tumor biopsy specimens obtained from 17 patients used as their own controls with and without leucovorin was performed. These studies reveal an increased stabilization of the 5-fluorodeoxyuridylate (FdUMP)-thymidylate synthase (TS) folate ternary complex with the addition of leucovorin. There was a 71% +/- 14% occupancy or inhibition of the enzyme with the use of both 5-FU and leucovorin, v 30% +/- 13% for 5-FU alone (P2 less than .037). The percent TS bound in responding patients was substantially higher than in those patients with progressive disease. Finally, the mean total tumor TS pre-therapy in seven patients was 31 fmol/mg compared with a mean of 81 fmol/mg in these same seven patients 24 hours after therapy. This 2.6-fold increase suggests that there is an induction of the enzyme, TS, with 5-FU treatment.