gebhart/patrepeval huggingface dataset:
The European Bioinformatics Institute (EBI) databases (1996)

The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource.The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva.Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available.The EBI network services include database searching and sequence similarity searching facilities.
Optical Coherence Tomography (1991)

A technique called optical coherence tomography (OCT) has been developed for noninvasive cross-sectional imaging in biological systems. OCT uses low-coherence interferometry to produce a two-dimensional image of optical scattering from internal tissue microstructures in a way that is analogous to ultrasonic pulse-echo imaging. OCT has longitudinal and lateral spatial resolutions of a few micrometers and can detect reflected signals as small as approximately 10(-10) of the incident optical power. Tomographic imaging is demonstrated in vitro in the peripapillary area of the retina and in the coronary artery, two clinically relevant examples that are representative of transparent and turbid media, respectively.
Silicon chemistry as a novel source of chemical diversity in drug design. (2003)

The use of organosilicon chemistry in drug design is reviewed. The field of bioorganosilicon chemistry, which sprung up in the 1970s to exploit the opportunities of silicon for drug design, is currently being developed into a practical and commercial enterprise. This review is mainly focused on two different approaches: (i) synthesizing a silicon analog of a known drug in which one carbon atom has been replaced by a silicon atom, with the rest of the molecule being identical (carbon/silicon switch, sila-substitution); (ii) synthesizing completely new silicon-based classes of compounds (the carbon analogs of which do not exist) that exploit specific features of silicon chemistry to address a well-validated target.
A Wortmannin-sensitive Signal Transduction Pathway Is Involved in the Stimulation of Insulin Release by Vasoactive Intestinal Polypeptide and Pituitary Adenylate Cyclase-activating Polypeptide (1996)

Vasoactive intestinal polypeptide (VIP), pituitary adenylate cyclase-activating polypeptide-27 (PACAP-27), and PACAP-38 stimulated insulin release with EC50 values of 0.15, 0.15, and 0.06 nM respectively, as expected for the VIP2/PACAP3 receptor subtype. Secretion was stimulated promptly and peaked at 6-10 min. At 30 min, the secretion rate was still 2-3-fold higher than the control rate. The peptides increased cyclic AMP and [Ca2+]i transiently so that at 30 min they had returned to control values. Therefore, an additional signal is required to explain the prolonged stimulation of release. The prolonged effects, but not the acute effects of VIP and PACAP on insulin release were inhibited by low concentrations of wortmannin, a phosphatidylinositol 3-kinase (PI 3-kinase) inhibitor. While wortmannin inhibited PI 3-kinase activity in cell lysates, no activation by the peptides was seen. Therefore, the wortmannin-sensitive pathway is either dependent on basal PI 3-kinase activity, or another target for wortmanin is responsible for inhibition of the peptide-stimulated secretion. It is concluded that the acute stimulation of insulin release by VIP and PACAP is mediated by increased cyclic AMP and [Ca2+]i, whereas the sustained release is mediated by a novel wortmannin-sensitive pathway.
S-RCAT (sphere-shaped-recess-channel-array transistor) technology for 70nm DRAM feature size and beyond (2005)

For the first time, S-RCAT (sphere-shaped-recess-channel-array transistor) technology has been successfully developed in a 2Gb density DRAM with 70nm feature size. It is a modified structure of the RCAT (recess-channel-array transistor) and shows an excellent scalability of recessed-channel structure to sub-50nm feature size. The S-RCAT demonstrated superior characteristics in DIBL, subthreshold swing (SW), body effect, junction leakage current and data retention time, comparing to the RCAT structure, in this paper, S-RCAT is proved to be the most promising DRAM array transistor suitable for sub-50nm and mobile applications.
Software smart cards via cryptographic camouflage (2003)

A sensitive point in public key cryptography is how to protect the private key. We outline a method of protecting private keys using cryptographic camouflage. Specifically, we do not encrypt the private key with a password that is too long for exhaustive attack. Instead, we encrypt it so that only one password will decrypt it correctly, but many passwords will decrypt it to produce a key that looks valid enough to fool an attacker. For certain applications, this method protects a private key against dictionary attack, as a smart card does, but entirely in software.
Uniform high frequency expression of autoantibody-associated crossreactive idiotypes in the primary B cell follicles of human fetal spleen. (1990)

At 23 wk of gestation, the fetal spleen contains follicles of lymphocytes that coexpress B cell differentiation antigens, surface Ig, and the 67-kD pan-T lymphocyte antigen, CD5 (Leu-1). Such cells are thought to represent the normal equivalent cells of B chronic lymphocytic leukemia (CLL). This B cell leukemia is distinctive in that high proportions of patients have leukemic cells that express sIg bearing one or more crossreactive idiotypes (CRIs) that commonly are found on IgM autoantibodies. We performed immunohistochemical studies on fetal spleen at 23 wk of gestation using a panel of mAbs specific for autoantibody-associated CRIs. We find that high proportions (5-17%) of the lymphocytes within each follicle react with any one of the anti-CRI mAbs. Furthermore, there is little variation between primary follicles in the proportions of cells that express a particular CRI. Using a cocktail of four anti-CRI mAbs, we detect autoantibody-associated CRIs on approximately one-third of the lymphocytes within each of the primary B cell follicles. These data indicate that the many of the Igs produced during early B cell development may be structurally related to IgM autoantibodies and to Ig expressed in CLL and related CD5 B cell malignancies. Furthermore, these studies suggest that the repertoire of Ig V genes expressed in each primary B cell follicle may be representative of the total restricted Ig V gene repertoire expressed during early B cell ontogeny.
The Simulator: Understanding Adaptive Sampling in the Moderate-Confidence Regime (2017)

We propose a novel technique for analyzing adaptive sampling called the {\em Simulator}. Our approach differs from the existing methods by considering not how much information could be gathered by any fixed sampling strategy, but how difficult it is to distinguish a good sampling strategy from a bad one given the limited amount of data collected up to any given time. This change of perspective allows us to match the strength of both Fano and change-of-measure techniques, without succumbing to the limitations of either method. For concreteness, we apply our techniques to a structured multi-arm bandit problem in the fixed-confidence pure exploration setting, where we show that the constraints on the means imply a substantial gap between the moderate-confidence sample complexity, and the asymptotic sample complexity as $δ\to 0$ found in the literature. We also prove the first instance-based lower bounds for the top-k problem which incorporate the appropriate log-factors. Moreover, our lower bounds zero-in on the number of times each \emph{individual} arm needs to be pulled, uncovering new phenomena which are drowned out in the aggregate sample complexity. Our new analysis inspires a simple and near-optimal algorithm for the best-arm and top-k identification, the first {\em practical} algorithm of its kind for the latter problem which removes extraneous log factors, and outperforms the state-of-the-art in experiments.
On the Survivability of Routing Protocols in Ad Hoc Wireless Networks (2006)

Survivable routing protocols are able to provide service in the presence of attacks and failures. The strongest attacks that protocols can experience are attacks where adversaries have full control of a number of authenticated nodes that behave arbitrarily to disrupt the network, also referred to as Byzantine attacks. This work examines the survivability of ad hoc wireless routing protocols in the presence of several Byzantine attacks: black holes, flood rushing, wormholes and overlay network wormholes. Traditional secure routing protocols that assume authenticated nodes can always be trusted, fail to defend against such attacks. Our protocol, ODSBR, is an on-demand wireless routing protocol able to provide correct service in the presence of failures and Byzantine attacks. We demonstrate through simulation its effectiveness in mitigating such attacks. Our analysis of the impact of these attacks versus the adversary’s effort gives insights into their relative strengths, their interaction and their importance when designing wireless routing protocols.
Production of Bispecific Antibodies: Diabodies and Tandem scFv (2012)

Recombinant bispecific antibodies have many different applications; especially promising is their therapeutic potential due to their ability to retarget an effector molecule or a cell to a disease-related target structure. In the last years, many formats have been developed: two commonly used are the bispecific diabody and the tandem scFv. In this chapter, the cloning, bacterial production, purification, and characterization of the two antibody formats are described in detail.
Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. (2001)

Blood samples are an excellent source of large amounts of genomic DNA. However, alternative sources are often needed in epidemiological studies because of difficulties in obtaining blood samples. This report evaluates the buccal cytobrush and alcohol-containing mouthwash protocols for collecting DNA by mail. Several DNA extraction techniques are also evaluated. The study was conducted in two phases. In phase 1, we compared cytobrush and mouthwash samples collected by mail in two different epidemiological studies: (a) cytobrush samples (n = 120) from a United States case-control study of breast cancer; and (b) mouthwash samples (n = 40) from a prospective cohort of male United States farmers. Findings from phase 1 were confirmed in phase 2, where we randomized cytobrush (n = 28) and mouthwash (n = 25) samples among participants in the breast cancer study to directly compare both collection methods. The median human DNA yield determined by hybridization with a human DNA probe from phenol-chloroform extracts was 1.0 and 1.6 microg/2 brushes for phases 1 and 2, respectively, and 27.5 and 16.6 microg/mouthwash sample for phases 1 and 2, respectively. Most (94-100%) mouthwash extracts contained high molecular weight DNA (>23 kb), in contrast to 55-61% of the brush extracts. PCR success rates for amplification of beta-globin gene fragments (268, 536, and 989 bp) were similar for cytobrush and mouthwash phenol-chloroform extracts (range, 94.4-100%). Also, we obtained high success rates in determining the number of CAG repeats in the androgen receptor gene, characterizing tetranucleotide microsatellites in six gene loci, and screening for mutations in the BRCA1/2 genes in a subset of phenol-chloroform DNA extracts. Relative to DNA extracted by phenol-chloroform from cytobrush samples, DNA extracted by NaOH had lower molecular weight, decreased PCR success rates for most assays performed, and unreliably high spectrophotometer readings for DNA yields. In conclusion, although DNA isolated from either mouthwash or cytobrush samples collected by mail from adults is adequate for a wide range of PCR-based assays, a single mouthwash sample provides substantially larger amounts and higher molecular weight DNA than two cytobrush samples.
Recent Studies of the Enzymic Synthesis of Ricinoleic Acid by Developing Castor Beans (1981)

Oleate Delta(12)-hydroxylase activity was measured in extracts of developing castor bean seeds. Most of the hydroxylase activity is associated with microsomes. However, when microsomes are washed, the activity is completely lost. Some (50%) of the activity can be restored by addition of the 100,000g supernatant to the washed microsomes. Supernatant extracts (100,000g) of developing safflower seeds are able to restore all (100%) of the hydroxylase activity to the washed castor bean microsomes. In addition, purified mammalian catalase can restore some (25%) of the activity to the microsomes but is not as effective as either castor bean or safflower 100,000g supernatants. The K(m) of the hydroxylase for oxygen is 4 micromolar. Inasmuch as the activity was not inhibited by high concentrations of either carbon monoxide or cyanide, neither the involvement of cytochrome P450 nor other cytochrome systems is suggested. The enzyme system was not saturated by oleoyl-CoA, even at concentrations as high as 200 micromolar. When [(14)C]oleoyl-CoA is supplied as a substrate, the acyl component is rapidly transferred to phosphatidylcholine (PC). Hydroxylation may occur on PC or on a lipid which receives its acyl component from PC. However, exogeneously added 2-[1-(14)C]oleoyl-PC was hydroxylated at a much lower rate than was [1-(14)C]oleoyl-CoA added as the primary substrate.
Prescription of Nonsteroidal Anti-inflammatory Drugs and Muscle Relaxants for Back Pain in the United States (2004)

Neither traditional NSAIDs, nor COX-2 inhibitors, nor muscle relaxants dominated prescriptions for back pain. However, a small number of individual drugs were attributable to most of the prescriptions for traditional NSAIDs or muscle relaxants. The prescription of some of the medications demonstrated wide variations across different regions or different racial and educational groups. More studies are needed to understand the source of the variations and what constitutes optimal prescribing.
Mitochondrial Membrane Potential Selects Hybridomas Yielding High Viability in Fed‐Batch Cultures (2002)

Prior research (Follstad, B. D.; Wang, D. I. C.; Stephanopoulos, G. Mitochondrial membrane potential differentiates cells resistant to apoptosis in hybridoma cultures. Eur. J. Biochem. 2000, 267, 6534-6540.) identified mitochondrial membrane potential (MMP) as a marker of hybridoma subpopulations resistant to apoptosis caused by a variety of apoptosis inducers. In this study, we investigated the viability of hybridoma cell cultures inoculated with cells of varying MMP in regular fed-batch operation. A hybridoma cell population was separated using FACS into subpopulations based on their mean mitochondrial membrane potential (MMP) as measured using the common mitochondrial stain, Rhodamine 123 (Rh123). These subpopulations showed dramatic differences in their apoptotic death kinetics. Fed-batches inoculated with a high MMP subpopulation reached higher viable cell concentrations and viabilities that were maintained for prolonged periods of time relative to fed-batches inoculated with low MMP subpopulations. These results underline the heterogeneous nature of hybridoma cell cultures and suggest that mitochondrial physiology is a critical parameter determining culture performance.
Preparation of a biochip on porous silicon and application for label‐free detection of small molecule‐protein interactions (2007)

A new approach for the preparation of a biochip on porous silicon and the application of the biochip for detection of small molecule-protein interactions with desorption/ionization on porous silicon (DIOS) was demonstrated. The galvanostatically etched porous silicon substrates were chemically modified firstly to yield carboxylic acid terminated surfaces, and then the protein was covalently attached to the surface through amide bonding. By applying a solution of candidate chemicals to the surface and a subsequent wash step, the masses of captured compounds could be analyzed by DIOS. DIOS has advantages of being a direct detection tool compared to the classic fluorescence or chemiluminescence methods, because the process of labeling molecules employed in the fluorescence or chemiluminescence methods can sometimes alert the properties of the labeled molecule. The recognition between proteins and their binding partners is efficient and selective. A good tolerance to disturbance and high enrichment factor of the biochip to the analytes was observed. As an on-chip-based approach, the demonstrated method has a potential to perform in a high-throughput format.
Life-Death Balance Within the Cell (1996)

Three separate research groups report in this issue of Science ( pages. 782 , 784 , andp. 787 ) that a cellular protein called nuclear factor kappa B (NF-κ B)blocks the programmed form of cell suicide known as apoptosis in several cell types. This finding has led to the suggestion that blocking NF-κ B in tumor cells might make them more vulnerable to drugs or radiation.
Bacterial Insecticidal Toxins (2004)

Over the years it has been important for humans to control the populations of harmful insects and insecticides have been used for this purpose in agricultural and horticultural sectors. Synthetic insecticides, owing to their various side effects, have been widely replaced by biological insecticides. In this review we attempt to describe three bacterial species that are known to produce insecticidal toxins of tremendous biotechnological, agricultural, and economic importance. Bacillus thuringiensis (BT) accounts for 90% of the bioinsecticide market and it produces insecticidal toxins referred to as delta endotoxins. The other two bacteria belong to the genera Photorhabdus and Xenorhabdus, which are symbiotically associated with entomopathogenic nematodes of the families Heterorhabditidae and Steinernematidae respectively. Whereas, Xenorhabdus and Photorhabdus exist in a mutualistic association with the entomopathogenic nematodes, BT act alone. BT formulations are widely used in the field against insects; however, over the years there has been a gradual development of insect resistance against BT toxins. No resistance against Xenorhabdus or Photorhabdus has been reported to date. More recently BT transgenic crops have been prepared; however, there are growing concerns about the safety of these genetically modified crops. Nematodal formulations are also used in the field to curb harmful insect populations. Resistance development to entomopathogenic nematodes is unlikely due to the physical macroscopic nature of infection. Xenorhabdus and Photorhabdus transgenes have not yet been prepared; but are predicted to be available in the near future. In this review we start with an overview of the synthetic insecticides and then discuss Bacillus thuringiensis, Xenorhabdus nematophilus, and Photorhabdus luminescens in greater detail.
Stability of TiB2 as a Diffusion Barrier on Silicon (1991)

The stability of low‐pressure chemical vapor‐deposited films has been investigated for their potenital use as diffusion barriers between Al or Cu metallurgy and the Si substrate during post‐metal annealing at temperatures ranging from 450–640°C for Al, and 500–800°C for Cu. Although no evidence of intermixing was observed via Rutherford backscattering spectroscopy (RBS) for samples rapid thermal‐annealing (RTA) up to 1080°C, pyramid‐shape pits in the Si, bounded by (111) planes, were observed using transmission electron microscopy for the samples annealed above 950°C. Secondary ion mass spectroscopy depth profiles of B in Si originating from the solid source suggested enhanced diffusion after RTA. According to RBS spectra coupled with scanning electron microscopy (SEM) examination, (pre‐annealed) stacks appeared to be stable up to 500°C for 30 min in forming gas. For the stacks with as‐deposited (amorphous) films, plan‐view SEM of showed very limited reaction with Al up to 600°C, in good agreement with sheet resistance measurements. The as‐deposited, amorphous films were superior diffusion barriers compared to the annealed, polycrystalline . No interaction took place between sputtered Cu and an underlying, amorphous film up to 750°C, 30 min in vacuum. Plan‐view SEM, RBS, and sheet resistance measurements showed that the structure started to break down at 775°C.
Regeneration of the Heart in Diabetes by Selective Copper Chelation (2004)

Heart disease is the major cause of death in diabetes, a disorder characterized by chronic hyperglycemia and cardiovascular complications. Although altered systemic regulation of transition metals in diabetes has been the subject of previous investigation, it is not known whether changed transition metal metabolism results in heart disease in common forms of diabetes and whether metal chelation can reverse the condition. We found that administration of the Cu-selective transition metal chelator trientine to rats with streptozotocin-induced diabetes caused increased urinary Cu excretion compared with matched controls. A Cu(II)-trientine complex was demonstrated in the urine of treated rats. In diabetic animals with established heart failure, we show here for the first time that 7 weeks of oral trientine therapy significantly alleviated heart failure without lowering blood glucose, substantially improved cardiomyocyte structure, and reversed elevations in left ventricular collagen and beta(1) integrin. Oral trientine treatment also caused elevated Cu excretion in humans with type 2 diabetes, in whom 6 months of treatment caused elevated left ventricular mass to decline significantly toward normal. These data implicate accumulation of elevated loosely bound Cu in the mechanism of cardiac damage in diabetes and support the use of selective Cu chelation in the treatment of this condition.
Online Monitoring of Ring-Opening Metathesis Polymerization of Cyclooctadiene and a Functionalized Norbornene (2006)

The kinetics and mechanisms involved in the ring-opening metathesis polymerization of 5-norbornene-2-yl acetate (NAc) and cyclooctadiene (COD) in dichloromethane (DCM) were quantified using automatic continuous online monitoring of polymerization (ACOMP). The results yielded time-dependent monomer conversion and the effects of temperature and reactant concentration, evolution of weight-average molecular mass Mw, and intrinsic viscosity [η]w. The evolution of the molecular mass was generally consistent with a “living” mechanism in a rapid first phase, where expected target masses for p(NAc) were met, but often revealed a secondary, slight degradative phase. In contrast, p(COD) yielded molar masses far below target values and generally showed a more pronounced degradative phase. These latter two phenomena for p(COD) appear to be symptomatic of a mechanism that shortens chains with concomitant increase in polydispersity. Furthermore, through a combination of Mw, viscosity, and concentration dependencies it was deduced that the slow degradative phase for both p(NAc) and p(COD) is due almost entirely to cross-metathesis reactions. A probabilistic analysis for cross-metathesis supports these assertions. Automatic continuous mixing (ACM) was used to measure second virial coefficients and intrinsic viscosity, and these are consistent with polymers having large solvent domains and strong interactions for p(NAc). In a further application, a second addition of monomer during reactions revealed that no observable termination takes place over time. Results were cross-checked by conventional multidetector gel permeation chromatography (GPC). Ultimately, this method should help in the control of reactions to produce highly specific polymers and architectures.