gebhart/patrepeval huggingface dataset:
The Crystal Structure of Human Argonaute2 (2012)

Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans.
Multicenter Trial of Collagraft as Bone Graft Substitute (1991)

Collagraft (Zimmer and Collagen Corporation) consists of a mixture of porous beads composed of 60% hydroxyapatite and 40% tricalcium phosphate ceramic and fibrillar collagen. When mixed with autogenous bone marrow, it serves as an effective bone graft substitute. Since September 1986, this material has been used in a multiclinic prospective trial, randomized against cancellous iliac crest autografts in the treatment of long bone fractures. To date, 267 patients have entered this study with 128 patients receiving cancellous autograft and 139 patients receiving Collagraft. At 6- and 12-month follow-ups, Collagraft appears to function as well as autogenous graft when used in the treatment of acute long bone fractures.
Generation of Recombinant Virus-Like Particles of Human and Non-Human Polyomaviruses in Yeast <i>Saccharomyces cerevisiae</i> (2002)

The developed heterologous yeast expression system is suitable for high-level production of polyomavirus VLPs. Yeast-derived VLPs are generally free of toxins, host cell DNA and proteins. These VLPs might be useful for the generation of new diagnostical tools, gene delivery systems and antiviral vaccines.
The Working Hours Of Hospital Staff Nurses And Patient Safety (2004)

The use of extended work shifts and overtime has escalated as hospitals cope with a shortage of registered nurses (RNs). Little is known, however, about the prevalence of these extended work periods and their effects on patient safety. Logbooks completed by 393 hospital staff nurses revealed that participants usually worked longer than scheduled and that approximately 40 percent of the 5,317 work shifts they logged exceeded twelve hours. The risks of making an error were significantly increased when work shifts were longer than twelve hours, when nurses worked overtime, or when they worked more than forty hours per week.
Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides (2003)

We have improved upon the methodology and dramatically shortened the time required for accurate assembly of 5- to 6-kb segments of DNA from synthetic oligonucleotides. As a test of this methodology, we have established conditions for the rapid (14-day) assembly of the complete infectious genome of bacteriophage X174 (5386 bp) from a single pool of chemically synthesized oligonucleotides. The procedure involves three key steps: (i). gel purification of pooled oligonucleotides to reduce contamination with molecules of incorrect chain length, (ii). ligation of the oligonucleotides under stringent annealing conditions (55 degrees C) to select against annealing of molecules with incorrect sequences, and (iii). assembly of ligation products into full-length genomes by polymerase cycling assembly, a nonexponential reaction in which each terminal oligonucleotide can be extended only once to produce a full-length molecule. We observed a discrete band of full-length assemblies upon gel analysis of the polymerase cycling assembly product, without any PCR amplification. PCR amplification was then used to obtain larger amounts of pure full-length genomes for circularization and infectivity measurements. The synthetic DNA had a lower infectivity than natural DNA, indicating approximately one lethal error per 500 bp. However, fully infectious X174 virions were recovered after electroporation into Escherichia coli. Sequence analysis of several infectious isolates verified the accuracy of these synthetic genomes. One such isolate had exactly the intended sequence. We propose to assemble larger genomes by joining separately assembled 5- to 6-kb segments; approximately 60 such segments would be required for a minimal cellular genome.
Intermolecular Forces in the Self‐Assembly of Peptide Amphiphile Nanofibers (2006)

Abstract Peptide amphiphile molecules (PAs) developed in our laboratory self‐assemble from aqueous media into three‐dimensional networks of bioactive nanofibers. Multiple non‐covalent interactions promote assembly of the supramolecular nanofibers and ultimately determine the bulk physical properties of the macroscopic gels. In this study, we use oscillatory rheology, Fourier‐transform infrared spectroscopy, and circular‐dichroism spectroscopy to better understand the assembly mechanism of a typical PA molecule known as PA‐1. Self‐assembly of PA‐1 is triggered by counterion screening and stabilized by van der Waals and hydrophobic forces, ionic bridging, and coordination and hydrogen bonding. The concentration, electronic structure, and hydration of counterions significantly influence self‐assembly and gel mechanical properties.
Solid-Phase Synthesis of 1,4-Benzodiazepine-2,5-diones. Library Preparation and Demonstration of Synthesis Generality (1997)

A general and expedient method has been developed for the solid-phase synthesis of 1,4-benzodiazepine-2,5-diones 1 from three commercially available components; anthranilic acids, α-amino esters, and alkylating agents. Reaction conditions have been developed to prepare either racemic compounds for lead identification efforts or optically pure compounds for lead optimization efforts. The incorporation of diverse functionality into the benzodiazepine products has also been demonstrated. On the basis of the scope and generality of the synthesis sequence, a library of 1,4-benzodiazepine-2,5-diones has been prepared from 11 alkylating agents, 12 anthranilic acids, and 19 α-amino esters (nine sets of enantiomeric pairs and glycine methyl ester hydrochloride). The library was prepared in a spatially separate format using a microtiter-based apparatus that is inexpensive and straightforward to construct from ordinary items found in an organic or bioorganic laboratory. The high quality of the 1,4-benzodiazepine-2,5-dione library has been demonstrated by evaluating representative compounds by HPLC analysis and 1H NMR.
Bacterial Genes Involved in Type I Secretion and Sulfation Are Required to Elicit the Rice Xa21-Mediated Innate Immune Response (2004)

Innate immunity to microorganisms relies on the specific sensing of pathogen-associated molecules by host recognition receptors. Whereas studies in animals have largely focused on the recognition of extracellular pathogen-associated molecules by the TLR (toll-like receptor) superfamily, few studies have been carried out in plants, and it is not understood how these molecules are secreted or modified. The rice Xa21 gene encodes a receptor-like kinase that provides immunity against strains of the bacterial pathogen Xanthomonas oryzae pv. oryzae carrying AvrXa21 activity. We identified four X. oryzae pv. oryzae genes that are required for AvrXa21 activity. raxA, raxB, and raxC encode proteins with similarity to a membrane fusion protein, an ATP-binding cassette transporter, and an outer membrane protein, respectively, of bacterial type I secretion systems. The fourth gene, raxST, encodes a sulfotransferase-like protein. Sequence analysis of three naturally occurring X. oryzae pv. oryzae strains no longer recognized by Xa21 revealed alterations in the raxST and raxA genes. The raxC gene complemented an Escherichia coli tolC mutant for secretion of a double glycine-leader peptide confirming the function of raxC in type I secretion. These results indicate that bacterial type I secretion is necessary for Xa21-mediated recognition and immunity and further suggest that type I secretion and modification of pathogen-associated molecules play an important role in triggering the innate immune response in rice.
V(D)J germline gene repertoire analysis of monoclonal D antibodies and the implications for D epitope specificity (2000)

Despite the potential for diversity, only a minority of V(H) and V(L) germline genes are used by anti-D. Consequently, V(H) and V(L) pairings and the resulting canonical structures are similarly restricted.
A Methodology for the Design of Robotic Hands with Multiple Fingers (2008)

This paper presents a methodology that has been applied for a design process of anthropomorphic hands with multiple fingers. Biomechanical characteristics of human hand have been analysed so that ergonomic and anthropometric aspects have been used as fundamental references for obtaining grasping mechanisms. A kinematic analysis has been proposed to define the requirements for designing grasping functions. Selection of materials and actuators has been discussed too. This topic has been based on previous experiences with prototypes that have been developed at the Laboratory of Robotics and Mechatronics (LARM) of the University of Cassino. An example of the application of the proposed method has been presented for the design of a first prototype of LARM Hand.
Procalcitonin in diagnosis of severe infections. (1996)

Increased serum concentration of procalcitonin (PCT) in limited number of paediatric patients with acute severe bacterial infections has been described previously. In a prospective study in 337 hospitalised adult patients fulfilling the SIRS-criteria, serum PCT was determined on admission and up to 9 days thereafter. Patients with microbiologically documented infection showed peak values of 30 ng/ml at day 3, which rapidly decreased to normal levels. Patients without sepsis revealed baseline values (0.1 ng/ml or lower). The validity criteria were calculated for several breakpoints of PCT. We detected an interval from 0.1 to 0.5 ng/ml under which a severe microbial infection is unlikely (sensitivity 91%, specificity 25%, positive predictive value 39%, negative predictive value 86%). An infection is most likely above 0.5 ng/ml (sensitivity 60%, specificity 79%, positive predictive value 61%, negative predictive value 78%). Between these two points an infection can neither be confirmed nor excluded. The excellent specificity and negative predictive value at a cut-off point of 0.5 ng/ml suggests that this test might be a useful parameter in the management of infectious diseases.
Enhanced expression of the yeast Ure2 protein in Escherichia coli: the effect of synonymous codon substitutions at a selected place in the gene. (1998)

The expression of the yeast Ure2 protein and its two N- and C-terminal HA-(YPYPVDYA) epitope and His-tag fusions has been enhanced in E. coli by selected silent mutagenesis of the URE2 gene. The two Arg-AGA codons at positions 253 and 254 of the URE2 gene coding sequence were exchanged by CGT codons accordingly. This has allowed an increased yield (up to 100-fold) of the full-length protein synthesized. Western blotting with HA-epitope-specific antibodies using N- and C-terminal Ure2p-HA(epitope)-His-tag fusion constructs confirmed the integrity of the recombinant proteins. The N-(C-) terminal tagged proteins were shown to possess biological activity of the natural Ure2 protein.
Fetal behavior in diabetic and nondiabetic pregnant women: An exploratory study (1999)

To characterize differential behavior and the relationship between maternal blood glucose levels and behavior in fetuses of diabetic (n = 10) and nondiabetic (n = 20) women at 33 and 36 weeks gestational age (GA), spontaneous changes in fetal heart rate (FHR), body and breathing movements, and vibroacoustic stimulus elicited (3 stimulus/3 no-stimulus control trials) FHR changes and body movements were compared. Measures of maternal blood glucose levels were obtained immediately following testing; measures varied within normal range. Spontaneous behaviors showed no differences between groups and no relationship to maternal blood glucose levels. Sensory stimulation elicited similar average peak FHR accelerations (M = 17.1/20.0 BPM) and average movement scores (2.0/2.6) across groups. In the diabetic group at 33 weeks GA, the nature of the FHR change over time, showed more varied patterns of response, a shorter latency to peak acceleration, was less organized, and less mature; as average maternal blood glucose levels increased, elicited body movements decreased. These findings suggest immaturity and differential functional development of sensory–motor response systems in fetuses of diabetic mothers. © 1999 John Wiley & Sons, Inc. Dev Psychobiol 35: 69–80, 1999
Site-selective protein conjugation at histidine (2018)

Site-selective conjugation generally requires both (i) molecular engineering of the protein of interest to introduce a conjugation site at a defined location and (ii) a site-specific conjugation technology. Three N-terminal interferon α2-a (IFN) variants with truncated histidine tags were prepared and conjugation was examined using a bis-alkylation reagent, PEG<sub>(10kDa)</sub>-mono-sulfone <b>3</b>. A histidine tag comprised of two histidines separated by a glycine (His<sub>2</sub>-tag) underwent PEGylation. Two more IFN variants were then prepared with the His<sub>2</sub>-tag engineered at different locations in IFN. Another IFN variant was prepared with the His-tag introduced in an α-helix, and required three contiguous histidines to ensure that two histidine residues in the correct conformation would be available for conjugation. Since histidine is a natural amino acid, routine methods of site-directed mutagenesis were used to generate the IFN variants from <i>E. coli</i> in soluble form at titres comparable to native IFN. PEGylation conversions ranged from 28-39%. A single step purification process gave essentially the pure PEG-IFN variant (>97% by RP-HPLC) in high recovery with isolated yields ranging from 21-33%. The level of retained bioactivity was strongly dependent on the site of PEG conjugation. The highest biological activity of 74% was retained for the PEG<sub>10</sub>-106(<b>H</b>G<b>H</b>G)-IFN variant which is unprecedented for a PEGylated IFN. The His<sub>2</sub>-tag at 106(<b>H</b>G<b>H</b>G)-IFN is engineered at the flexible loop most distant from IFN interaction with its dimeric receptor. The biological activity for the PEG<sub>10</sub>-5(<b>H</b>G<b>H</b>)-IFN variant was determined to be 17% which is comparable to other PEGylated IFN conjugates achieved at or near the N-terminus that have been previously described. The lowest retained activity (10%) was reported for PEG<sub>10</sub>-120(<b>HHH</b>)-IFN which was prepared as a negative control targeting a IFN site thought to be involved in receptor binding. The presence of two histidines as a His<sub>2</sub>-tag to generate a site-selective target for bis-alkylating PEGylation is a feasible approach for achieving site-selective PEGylation. The use of a His<sub>2</sub>-tag to strategically engineer a conjugation site in a protein location can result in maximising the retention of the biological activity following protein modification.
Department 1824 Job Card System: A new web-based business tool (1998)

The Analytical Chemistry Department uses a system of job cards to control and monitor the work through the organization. In the past, many different systems have been developed to allow each laboratory to monitor their individual work and report data. Unfortunately, these systems were separate and unique which caused difficulty in ascertaining any overall picture of the Department`s workload. To overcome these shortcomings, a new Job Card System was developed on Lotus Notes/Domino{trademark} for tracking the work through the laboratory. This application is groupware/database software and is located on the Sandia Intranet which allows users of any type of computer running a network browser to access the system. Security is provided through the use of logons and passwords for users who must add and/or modify information on the system. Customers may view the jobs in process by entering the system as an anonymous user. An overall view of the work in the department can be obtained by selecting from a variety of on screen reports. This enables the analysts, customers, customer contacts, and the Department Manager to quickly evaluate the work in process, the resources required, and the availability of equipment. On-line approval of the work and e-mail messaging of completed jobs has been provided to streamline the review and approval cycle. This paper provides a guide for the use of the Job Card System and information on maintenance of the system.
Anthranilate Repellency to Starlings: Chemical Correlates and Sensory Perception (1989)

J. Russell Mason, Michael A. Adams, Larry Clark, Anthranilate Repellency to Starlings: Chemical Correlates and Sensory Perception, The Journal of Wildlife Management, Vol. 53, No. 1 (Jan., 1989), pp. 55-64
<p>Out of the Clinic, into the Home: The in-Home Use of Phantom Motor Execution Aided by Machine Learning and Augmented Reality for the Treatment of Phantom Limb Pain</p> (2020)

Our findings suggest that adherence to treatment, and thus related outcomes, could be further improved by considering disparate user types and their utilization patterns. Our study highlights the importance of understanding, from multiple disciplinary angles, the tight coupling and interplay between pain, perceived need, and use of medical devices in patient-initiated therapy.
Long-Term Protective Immunity of Recipients of the OKA Strain of Live Varicella Vaccine (1985)

In spite of close contacts with patients who had varicella, 101 of 106 (95%) healthy and sick children (142 of 147 (97%) exposures of these children) who had received the OKA strain of live varicella vaccine 7 to 10 years earlier were protected against the disease completely. Among them, 37 of 38 (97%) vaccine recipients who received immunologic testing had varicella-zoster virus (VZV) antibodies tested by fluorescent antibody to membrane antigen method with a geometric mean titer of 1:9.3, and 37 of the 38 (97%) showed positive skin reaction to varicella-zoster virus antigen with erythema (mean diameter 13.4 mm). These findings were compared with those for 29 children who had contracted typical varicella 7 to 10 years earlier, whose seropositive rate was 100% with a geometric mean titer of 1:10.5, and 97% of whom (28/29) had positive skin reaction with mean diameter of 12.9 mm. These results indicate that the vaccine-induced protective immunity persists for approximately one decade and is almost equal to the long-term immunity following natural infection.
Intensity correction with a pair of spoiled gradient recalled echo images (2009)

Intensity inhomogeneities in magnetic resonance images (MRI) are a frequently occurring artefact, and result in the same tissue class to have vastly different intensities within an image. These inhomogeneities can be modelled by a slowly varying field, which is also called the bias field. Previous phantom-, image- or sequence based approaches suffer from long scan times, post-processing times or do not sufficiently remove the intensity variations. These intensity variations cause problems for quantitative image analysis algorithms (segmentation, registration) as well as clinicians (e.g. by complicating the visual assessment). This paper presents a novel technique (COIN, correction of intensity inhomogeneities) that uses two calibration images (fast spoiled gradient echo) to map a parameter containing the bias field, which is specific to the patient during a particular exam. This parametric map can then be used to correct any other images acquired during the same exam, regardless of the sequence employed. By using a short repetition time (less than 5 ms) for the calibration scans, the additional scan time is reduced to 60 s (max). The subsequent post-processing time is approximately 60 s per 20 slices. We successfully validate our approach on simulated brain MRI as well as real liver and spinal images. These images were acquired with a number of different coils, sequences and weightings. A comparison of our method with an existing, commercially available algorithm by radiologists shows that COIN is superior.
<title>Automatic shearography inspection systems for aircraft components in production</title> (1999)

Shearography has been validated as fast and reliable inspection technique for composite materials in aerospace components. Following a several years phase of evaluation of the technique to show the principal applicability and prove the required sensitivity, now the first production lines for aerospace components have been equipped with automatic shearography inspection systems. In this paper, recent installations of automatic inspection systems in aerospace industries are presented.
Synthesis of an organoinsulin molecule that can be activated by antibody catalysis (2001)

We have developed a methodology of prodrug delivery by using a modified insulin species whose biological activity potentially can be regulated in vivo. Native insulin was derivatized with aldol-terminated chemical modifications that can be selectively removed by the catalytic aldolase antibody 38C2 under physiologic conditions. The derivatized organoinsulin (insulin(D)) was defective with respect to receptor binding and stimulation of glucose transport. The affinity of insulin(D) for the insulin receptor was reduced by 90% in binding studies using intact cells. The ability of insulin(D) to stimulate glucose transport was reduced by 96% in 3T3-L1 adipocytes and by 55% in conscious rats. Incubation of insulin(D) with the catalytic aldolase antibody 38C2 cleaved all of the aldol-terminated modifications, restoring native insulin. Treatment of insulin(D) with 38C2 also restored insulin(D)'s receptor binding and glucose transport-stimulating activities in vitro, as well as its ability to lower glucose levels in animals in vivo. We propose that these results are the foundation for an in vivo regulated system of insulin activation using the prohormone insulin(D) and catalytic antibody 38C2 with potential therapeutic application.
Interaction of Peptides with Sequences from the Newcastle Disease Virus Fusion Protein Heptad Repeat Regions (1999)

Typical of many viral fusion proteins, the sequence of the Newcastle disease virus (NDV) fusion protein has several heptad repeat regions. One, HR1, is located just carboxyl terminal to the fusion peptide, while the other, HR2, is located adjacent to the transmembrane domain. The structure and function of a synthetic peptide with a sequence from the region of the NDV HR1 region (amino acids 150 to 173) were characterized. The peptide inhibited fusion with a half-maximal concentration of approximately 2 microM; however, inhibition was observed only if the peptide was added prior to protease activation of the fusion protein. This inhibition was virus specific since the peptide had minimal effect on fusion directed by the Sendai virus glycoproteins. To explore the mechanism of action, the potential HR1 peptide interaction with a previously characterized fusion inhibitory peptide with a sequence from the HR2 domain (J. K. Young, R. P. Hicks, G. E. Wright, and T. G. Morrison, Virology 238:291-304, 1997) was characterized. The results demonstrated an interaction between the two peptides both functionally and directly. First, while the individual peptides each inhibit fusion, equimolar mixtures of the two peptides had minimal effect on fusion, suggesting that the two peptides form a complex preventing their interaction with a target protein. Second, an HR2 peptide covalently linked with biotin was found to bind specifically to HR1 peptide in a Western blot. The structure of the HR1 peptide was analyzed by nuclear magnetic resonance spectroscopy and found to be an alpha helix.