gebhart/patrepeval huggingface dataset:
Supplemental ascorbate in the supportive treatment of cancer: Reevaluation of prolongation of survival times in terminal human cancer (1978)

A study has been made of the survival times of 100 terminal cancer patients who were given supplemental ascorbate, usually 10 g/day, as part of their routine management and 1000 matched controls, similar patients who had received the same treatment except for the ascorbate. The two sets of patients were in part the same as those used in our earlier study [Cameron, E. & Pauling, L. (1976) Proc. Natl. Acad. Sci. USA 73, 3685-3689]. Tests confirm that the ascorbate-treated patients and the matched controls are representative subpopulations of the same population of "untreatable" patients. Survival times were measured not only from the date of "untreatability" but also from the precisely known date of first hospital attendance for the cancer that eventually reached the terminal stage. The ascorbate-treated patients were found to have a mean survival time about 300 days greater than that of the controls. Survival times greater than 1 yr after the date of untreatability were observed for 22% of the ascorbate-treated patients and for 0.4% of the controls. The mean survival time of these 22 ascorbate-treated patients is 2.4 yr after reaching the apparently terminal stage; 8 of the ascorbate-treated patients are still alive, with a mean survival time after untreatability of 3.5 yr.
Coarse-grained lattice protein folding on a quantum annealer (2018)

Lattice models have been used extensively over the past thirty years to examine the principles of protein folding and design. These models can be used to determine the conformation of the lowest energy fold out of a large number of possible conformations. However, due to the size of the conformational space, new algorithms are required for folding longer proteins sequences. Preliminary work was performed by Babbush et al. (2012) to fold a small peptide on a planar lattice using a quantum annealing device. We extend this work by providing improved Ising-type Hamiltonian encodings for the problem of finding the lowest energy conformation of a lattice protein. We demonstrate a decrease in quantum circuit complexity from quadratic to quasilinear in certain cases. Additionally, we generalize to three spatial dimensions in order to obtain results with higher correlation to the actual atomistic 3D structure of the protein and outline our heuristic approach for splitting large problem instances into smaller subproblems that can be directly solved with the current D-Wave 2000Q architecture. To the best of our knowledge, this work sets a new record for lattice protein folding on a quantum annealer by folding Chignolin (10 residues) on a planar lattice and Trp-Cage (8 residues) on a cubic lattice.
Democracy-Independence Trade-Off in Oscillating Dendrites and Its Implications for Grid Cells (2010)

Dendritic democracy and independence have been characterized for near-instantaneous processing of synaptic inputs. However, a wide class of neuronal computations requires input integration on long timescales. As a paradigmatic example, entorhinal grid fields have been thought to be generated by the democratic summation of independent dendritic oscillations performing direction-selective path integration. We analyzed how multiple dendritic oscillators embedded in the same neuron integrate inputs separately and determine somatic membrane voltage jointly. We found that the interaction of dendritic oscillations leads to phase locking, which sets an upper limit on the timescale for independent input integration. Factors that increase this timescale also decrease the influence that the dendritic oscillations exert on somatic voltage. In entorhinal stellate cells, interdendritic coupling dominates and causes these cells to act as single oscillators. Our results suggest a fundamental trade-off between local and global processing in dendritic trees integrating ongoing signals.
CuBr/<i>rac</i>-BINOL-Catalyzed <i>N</i>-Arylations of Aliphatic Amines at Room Temperature (2006)

We have developed an efficient and readily available catalyst system CuBr/racemic BINOL (1,1'-binaphthyl-2,2'-diol) that catalyzes N-arylation of aliphatic amines at room temperature, and this inexpensive catalyst system is of high selectivity and tolerance toward various functional groups in the substrates.
Topology API Use Cases (2013)

This document describes use cases for gathering routing, forwarding
and policy information, (hereafter referred to as topology
information), about the network. It describes several applications
that need to view the topology of the underlying physical or logical
network. This document further demonstrates a need for a Topology
Manager and related functions that collects topology data from
network elements and other data sources, coalesces the collected data
into a coherent view of the overall network topology, and normalizes
the network topology view for use by clients -- namely, applications
that consume topology information.
Relapses in multiple sclerosis are age- and time-dependent (2008)

Relapse rates were age- and time-dependent. Our observations have clinical implications: 1) any drug able to modify relapse rates has the greatest potential for a population impact in patients <40 years old and within the first few demi-decades of disease; 2) continuation of drug beyond these times may be of limited value; 3) long-term follow-up studies must consider that relapse rates probably decline at different rates over time according to the patient's onset age; 4) a relapse-quiescent period in MS is not uncommon.
Abnormal hemoglobins in a quarter million people (1976)

Hemolysates of erythrocytes from more than a quarter million people in Alabama were electrophoresed on cellulose acetate, pH 8.4, and those samples exhibiting an abnormality were also electrophoresed in citrate agar, pH 6.0. The globin chains of mutants other than Hb S and C were electrophoresed in urea-mercaptoethanol buffers at both pH 8.9 and pH 6.0, and 60 of them were also analyzed structurally. Of about 6000 samples from whites, only three contained abnormal hemoglobins--Hb D Los Angeles, Hb J Baltimore, and one unidentified. Of 249,000 samples from blacks, about 29,000 contained electrophoretically detectable abnormalities, most of them associated with Hb S or C, present in a frequency of about 9% and 3%, respectively. About 1000 samples resolved into patterns of potential clinical significance. Twenty other mutant hemoglobins were detected, in various genetic combinations in 164 kindreds; four of these-Hb Alabama, Montgomery, Titusville, and Mobile-- were previously unknown. The methods used are rapid, economical, and well suited for large scale surveys. They provide highly specific characterizations of many mutant hemoglobins, and no discrepancies were found between the presumptive identifications based on these characterizations and the definitive identifications obtained from structural analyses.
Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid–Peptide Chimeras (2018)

Striking synergy between nucleic acids and proteins is exhibited in living cells. Whether such mutual activity can be performed using simple supramolecular nucleic acid-peptide (NA-pep) architectures remains a mystery. To shed light on this question, we studied the emergence of a primitive synergy in assemblies of short DNA-peptide chimeras. Specifically, we characterized multiple structures forming along gradual mixing trajectory, in which a peptide solution was seeded with increasing amounts of NA-pep chimeras. We report on the systematic change from β-sheet-peptide-based fibrillar architectures into the spherical structures formed by the conjugates. Remarkably, we find that through forming onion-like structures, the conjugates exhibit increased DNA hybridization stability and bind small molecules more efficiently than the peptides or DNA alone. A brief discussion highlights the implications of our findings for the production of new materials and for research on the origin of life.
Explaining World Wide Web Traffic Self-Similarity (1995)

Recently the notion of self-similarity has been shown to apply to wide-area and local-area network traffic. In this paper we examine the mechanisms that give rise to self-similar network traffic. We present an explanation for traffic self-similarity by using a particular subset of wide area traffic: traffic due to the World Wide Web (WWW). Using an extensive set of traces of actual user executions of NCSA Mosaic, reflecting over half a million requests for WWW documents, we show evidence that WWW traffic is selfsimilar. Then we show that the self-similarity in such traffic can be explained based on the underlying distributions of WWW document sizes, the effects of caching and user preference in file transfer, the effect of user &quot;think time&quot;, and the superimposition of many such transfers in a local area network. To do this we rely on empirically measured distributions both from our traces and from data independently collected at over thirty WWW sites. 1 Introduction Understanding the ...
Inhibition of WEE1 kinase and cell cycle checkpoint activation sensitizes head and neck cancers to natural killer cell therapies (2018)

Tumor cell resistance to granzyme B-induced cell death can be reversed through inhibition of WEE1 kinase as AZD1775 sensitized both murine and human head and neck cancer cells to NK lysis. These data provide the pre-clinical rationale for the combination of small molecules that reverse cell cycle checkpoint activation and NK cellular therapies.
PARQ - a system supporting information networking over HF radio links (1997)

The use of narrowband HF as a medium for information transfer in a networked environment has traditionally been viewed as limited due to the inherent problems of relatively high bit-error rates and low data throughputs. This paper provides a description of the Physical-layer Automatic Repeat reQuest (PARQ) protocol which addresses these two fundamental problems. Errors in delivered data are effectively eliminated by the ARQ component of the protocol, while the throughput is maximised by selecting the optimal raw channel data rate. Details of PARQ's design parameters and implementation are given along with initial laboratory and field testing results. The paper concludes with a brief discussion of future system enhancements.
Nonlinear actuator fault detection and isolation for a VTOL aircraft (2001)

The recently introduced geometric approach to the nonlinear fault detection and isolation problem is used to detect actuator faults for the vertical takeoff and landing aircraft. The approach leads to a filter which, by processing the outputs of the plant, detects the faults and distinguishes which one is occurring.
Model Simulation and Analysis of Perfusion Culture of Mammalian Cells at High Cell Density (1999)

Rate equations recently proposed by the authors for growth, death, consumption of nutrients, and formation of lactic acid, ammonium, and monoclonal antibody of hybridoma cells are used to simulate and analyze the behavior of perfusion cultures. Model simulations are in good agreement with experimental results from three different cell lines under varied perfusion and cell bleed rates except for cultures with very low viability. Analysis of simulations and experimental results indicates that in perfusion cultures with a complete cell separation cell bleed rate is a key parameter that strongly affects all the process variables, whereas the perfusion rate mainly affects the total and viable cell concentrations and the volumetric productivity of monoclonal antibody. Growth rate, viability, and specific perfusion rate of cells are only a function of the cell bleed rate. This also applies to cultures with partial cell separation in the permeate if the effective cell bleed rate is considered. It is suggested that the (effective) cell bleed rate of a perfusion culture should be carefully chosen and controlled separately from the perfusion rate. In general, a low cell bleed rate that warrants a reasonable cell viability appears to be desirable for the production of antibodies. Furthermore, model simulations indicate the existence of an optimum initial glucose concentration in the feed. For the cell lines considered, the initial glucose concentration used in normal cell culture media is obviously too high. The initial glutamine concentration can also be reduced to a certain extent without significantly impairing the growth and antibody production but considerably reducing the ammonia concentration. The mathematical model can be used to predict these optimum conditions and may also be used for process design.
TUMOUR CHEMOTHERAPY V.SYNTHESIS OF SOME o-SUBSTITUTED p-[BIS-(2-CHLOROETHYL)-AMINO]-PHENYLALANINE (1960)

p-[Bis-(2-chloroethyl)-amino]-phenylalanine (Ⅰ,Sarcolysine, Melphalen) shows pronounced activity against certain tumours. Recently, m-[bis-(2-chloroethyl)-amino]-phenylalanine (Ⅱ) was reported to be more favorable in chemotherapeutic index. β-{p-[Bis-(2-chloroethyl)-amino]-phenyl}-β-amino-propionic acid (Ⅲ) possesses activity against certain tumour cells.In the present investigation, the synthesis of some o-substituted p-[bis-(2-chloroethyl)-amino]-phenylalanine (Ⅳ:Ⅳa,Ⅳb,Ⅳc,Ⅳd andⅣe) from corresponding o-substituted-p-nitrotoluene(Ⅴ) was described. Compound Ⅴ was brominated with N-bromo-succinimide to give Ⅵ. The latter was condensed with ethyl formamido (or acetamido) malonate, forming ethyl formamido-(or acetamido)-o-substituted p-nitrobenzyl-malonate (Ⅶ). Compound Ⅶ was reduced to the corresponding amino compound Ⅷ by catalytic hydrogenation, the latter was then hydroxy-ethylated with ethylene oxide to give bis-(2-hydroxyethyl)-amino compound Ⅸ, which was converted to Ⅹ on treatment with thionyl chloride or phosphorus oxychloride. Compound Ⅹ was subjected to hydrolysis and decarboxylation in boiling hydrochloric acid to yield Ⅳ.The preparation of two dipeptides, Ⅺ and Ⅻ, has also been described.o-Methoxy-p-[bis-(2-chloroethyl)-amino]-phenylalanine(Ⅳa) exhibited marked inhibition against sarcoma 180, Ehrlich ascites carcinoma, Guerin's carcinoma, etc. The pharmacological examination of the other compounds is in progress.
Breeding objectives for pulp production of <i>Eucalyptus</i><i>globulus</i> under different industrial cost structures (1993)

Breeding objectives were defined for pulp production of Eucalyptusglobulus Labill, using a simple profit equation relating the monetary cost savings per tonne of pulp produced with stem volume, wood density, and pulp yield. The economic importance of each trait was calculated for five different pulp and forestry industry scenarios with widely different cost structures. Selection indices integrating various combinations of volume growth, wood density, and pulp yield were compared for their ability to meet the different breeding objectives. There was surprising consistency in results across the range of breeding objectives and cost structures studied. It was clear that selection indices integrating volume, wood density, and pulp yield gave the most accurate selection and maximized genetic gain in breeding objectives. The cost savings from indices that included only volume were always much less than one-half, and sometimes as low as one-quarter, as much as those from indices integrating volume and wood traits. In the case study considered, E. globulus in Portugal, these cost savings had substantial implications for company profitability.
Analysis of the Hosts and Transmission Paths of SARS-CoV-2 in the COVID-19 Outbreak (2020)

The severe respiratory disease COVID-19 was initially reported in Wuhan, China, in December 2019, and spread into many provinces from Wuhan. The corresponding pathogen was soon identified as a novel coronavirus named SARS-CoV-2 (formerly, 2019-nCoV). As of 2 May, 2020, over 3 million COVID-19 cases had been confirmed, and 235,290 deaths had been reported globally, and the numbers are still increasing. It is important to understand the phylogenetic relationship between SARS-CoV-2 and known coronaviruses, and to identify its hosts for preventing the next round of emergency outbreak. In this study, we employ an effective alignment-free approach, the Natural Vector method, to analyze the phylogeny and classify the coronaviruses based on genomic and protein data. Our results show that SARS-CoV-2 is closely related to, but distinct from the SARS-CoV branch. By analyzing the genetic distances from the SARS-CoV-2 strain to the coronaviruses residing in animal hosts, we establish that the most possible transmission path originates from bats to pangolins to humans.
COMPUTER-AIDED PHOTOGRAPH MATCHING IN STUDIES USING INDIVIDUAL IDENTIFICATION: AN EXAMPLE FROM SERENGETI CHEETAHS (2001)

Photographic identification of naturally marked animals is a powerful and nonintrusive technique for obtaining information on behavior, population size, and life-history parameters in wild populations. Yet handling large quantities of photographs is time consuming and prone to error. Computer-aided matching can limit the number of photographs that must be examined visually to confirm that 2 sightings are the same individual. To identify individuals, I used a 3-dimensional (3-D) computer-matching system to aid in matching nearly 10,000 photographs of Serengeti cheetahs, Acinonyx jubatus, taken over 25 years. Accuracy in matching 2 photographs increased to 100% as the computer-generated similarity coefficient increased to 0.600 on a scale from 0 to 1. Probability of missing a match decreased to 6.4% when I used a threshold of similarity of 0.450. Poor quality of photographs decreased accuracy and resulted in up to 33% of matches being missed. Comparisons of photographs at skewed camera angles generally reduced similarity coefficients. Similarity coefficients were no higher for related or unrelated animals, suggesting that the technique is not appropriate for distinguishing subtle similarities. Because 3-D computer-aided matching does not require familiarity with distinctive features of the particular study animal, it is robust to matcher inexperience. This technique can be modified for other species that have complex and variable pelage patterns.
CD23 expression in transformed small lymphocytic lymphomas/chronic lymphocytic leukemias and blastic transformations of mantle cell lymphoma. (1997)

The immunophenotypic marker, CD23, has been shown to be a useful marker for the distinction of small lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL) from mantle cell lymphoma (MCL). The usefulness of this marker has not previously been analyzed in distinguishing various "large cell" transformations of SLL/CLL from blastic transformations of MCL (MCL-B). Thirteen cases of transformed SLL/CLL and six cases of MCL-B were analyzed for expression of CD23, either by flow cytometry of peripheral blood, bone marrow, or fresh tissue or by immunoperoxidase staining of paraffin-embedded archival tissue. All of the 13 cases of transformed SLL/ CLL expressed CD23 and all of the 6 cases of MCL-B were negative for CD23. Therefore, CD23 is retained in transformed SLL/CLL. It is a useful marker in distinguishing transformed SLL/CLL from MCL-B and thus might aid in distinguishing those cases that present de novo without a previous diagnosis of SLL/CLL or MCL.
Piezoelectromagnetic smart structures (2004)

A piezoelectromagnetic medium is formed by bonding piezoelectric and magnetostrictive layers on tapered beams. Piezoelectromagnetic materials are often utilized as intelligent media in the design of distributed sensors and actuators of smart structures. A spectral finite element model is presented for evaluating the voltage and magnetic response of flexible structures subjected to modulated force input. The Taguchi methodology is applied as a robust design technique to study the effect of design variables such as the thickness of the magnetostrictive and piezoelectric layers, the taper ratio of the tapered beam and the boundary conditions. From the study it is concluded that the thickness of the magnetostrictive and piezoelectric layers and the taper ratio of the beam contribute significantly to the response of the structure considered.
Transition Metal Derivatives of Peptide Nucleic Acid (PNA) OligomersSynthesis, Characterization, and DNA Binding (2000)

This work describes the first automated solid-phase synthesis of metal derivatives of peptide nucleic acid (PNA) oligomers and their interaction with DNA and PNA. PNA constitutes a relatively young and very promising class of DNA analogues with excellent DNA and RNA binding properties. However, PNA lacks a suitable handle that would permit its sensitive detection on its own as well as when hybridized with complementary oligonucleotides. Metal complexes, on the other hand, offer high potential as markers for biomolecules. In this paper, we describe the synthesis of PNA heptamers (tggatcg-gly, where gly is a C-terminal glycine carboxylic acid amide) with two covalently attached metal complexes at the PNA N-terminus, namely a ferrocene carboxylic acid derivative and a tris(bipyridine)ruthenium(II) derivative. We show how all synthesis steps may be carried out with high yield on a DNA synthesizer, including attachment of the metal complexes. The conjugates were characterized by HPLC (>90% purity) and ESI-MS. Binding studies of the purified Ru-PNA heptamer to complementary DNA and PNA and comparison to the isosequential metal-free acetyl PNA heptamer proves that the attached metal complex has an influence on the stability (UV-T(m)) and structure (CD spectroscopy) of the conjugates, possibly by disruption of the nearby A:T base pair.
An 850 MHz current feedback operational amplifier (2003)

A monolithic DC-to-850 MHz, low-distortion current feedback operational amplifier fabricated in a complementary bipolar bonded wafer technology is described. Discussed are an approach for achieving low-input offset voltage without sacrificing common-mode range or gain bandwidth; design for expected package and board parasitics; the use of low-overhead, high-impedance signal mirrors in the gain stage; and inverting input bias current cancellation. The output clamp is described. A summary of the circuit's performance obtained from production and bench testing on multiple fabrication lots is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Alternative Approach to Generate shRNA from cDNA (2005)

Short hairpin RNA (shRNA) synthesized from vector-based expression is as effective as short interfering RNA (siRNA) synthesized in vitro for suppressing the expression of their corresponding genes. Recently, three groups independently reported a new technology to construct an shRNA library from cDNA, providing great hope for genome-wide functional screens in many biological systems. In the present study, we report an alternative approach to generate shRNA from cDNA. A major improvement was to use a nicking enzyme to open up the double-stranded DNA so that the loop region remains single-stranded while the rest of the DNA fragment is double-stranded at an elevated temperature (e.g., 72 degrees C). The single-stranded DNA was then converted into double-stranded DNA by Taq DNA polymerase using the existing strand in the double-stranded region as a primer. Thus, the extended product carried a palindromic structure of 19 bp separated by a loop. Finally, the DNA fragment was cloned into a vector that carries an H1 promoter at the upstream region and ends with 5Ts, a terminator for the Pol III polymerase, at the downstream region. To prove the principle, we constructed shRNA from green fluorescent protein (GFP) cDNA and successfully suppressed GFP expression. Consequently, this simplified approach provides a better alternative to generate shRNA libraries from cDNA. Such shRNA libraries can be used to identify potential siRNA target sequences and study gene functions by a variety of selection methods.