gebhart/patrepeval huggingface dataset:
Novel codon-optimized mini-intronic plasmid for efficient, inexpensive and xeno-free induction of pluripotency (2015)

The development of human induced pluripotent stem cell (iPSC) technology has revolutionized the regenerative medicine field. This technology provides a powerful tool for disease modeling and drug screening approaches. To circumvent the risk of random integration into the host genome caused by retroviruses, non-integrating reprogramming methods have been developed. However, these techniques are relatively inefficient or expensive. The mini-intronic plasmid (MIP) is an alternative, robust transgene expression vector for reprogramming. Here we developed a single plasmid reprogramming system which carries codon-optimized (Co) sequences of the canonical reprogramming factors (Oct4, Klf4, Sox2, and c-Myc) and short hairpin RNA against p53 ("4-in-1 CoMiP"). We have derived human and mouse iPSC lines from fibroblasts by performing a single transfection. Either independently or together with an additional vector encoding for LIN28, NANOG, and GFP, we were also able to reprogram blood-derived peripheral blood mononuclear cells (PBMCs) into iPSCs. Taken together, the CoMiP system offers a new highly efficient, integration-free, easy to use, and inexpensive methodology for reprogramming. Furthermore, the CoMIP construct is color-labeled, free of any antibiotic selection cassettes, and independent of the requirement for expression of the Epstein-Barr Virus nuclear antigen (EBNA), making it particularly beneficial for future applications in regenerative medicine.
Neuroendoscopy combined with frameless neuronavigation (2000)

Minimal invasive neurosurgery is becoming more and more standard in neurosurgical procedures. Several types of lesions are now approached endoscopically. The surgical planning and intraoperative orientation during endoscopic surgical procedures are sometimes difficult. To solve this problem, a combination of the endoscopic procedure with a frameless, armless neuronavigation system is used in our service. The combination of the endoscope and the frameless navigation system was used in tumour surgery, ventriculostomies and arachnoid cyst operations. All procedures were performed successfully. The combination of both systems has proved to be advantageous because of safe surgical planning using the frameless stereotactic technique and the possibility of real time orientation of the endoscope. This technique is very useful in removing intraventricular and large brain mass lesions.
Quality of life of women with endometriosis: comparison between epiphenomenon and severe disease (2012)

Purpose To compare pain symptoms and quality of life between epiphenomenon and endometriosis disease. Methods Between January 2004 and July 2008, 536 new cases of endometriosis confirmed by surgical biopsy were included in this observational cohort study (Auvergne Regional Cohort of Endometriosis). Questionnaires and visual analog scale scores for dysmenorrhoea, dyspareunia, chronic pelvic pain, premenstrual dysuria and dyschesia, quality of life instruments (SF-36), and sexual activity questionnaires were compared between group A (epiphenomenon group: 119 patients) and group B (endometriosis disease group: 318 patients with deep ovarian endometrioma and/or deep infiltrating nodules). Primary outcome was patient-reported pain rates. Secondary outcomes included quality-of-life tools. Results In cases of severe endometriosis, more pain at defecation and more dysmenorrhoea were observed than in cases of minimal endometriosis. The social repercussions and deterioration in quality of life were also affected, without any distinction between group A and B except for physical limitations. Quality of sex life was also affected in both groups. Conculsions This study confirms the ubiquitous pain symptoms of endometriosis. The lack of any correlation between functional symptomatology and anatomic severity of disease underlines how important it is not to neglect patients presenting what is called “minimal” endometriosis.
Ritanserin-induced changes in sleep-waking phases in rats. (1995)

Ten male Wistar rats were chronically implanted with conventional electrodes for sleep-waking stages detection. Three 12-hour electroencephalographic (EEG) registrations were performed once a week, after i.p. injection of the serotonin-2 (5-HT2) antagonist ritanserin at two doses (0.63 mg/kg and 2.5 mg/kg) and after ritanserin vehicle. The goal of the present study was to examine the effects of ritanserin on sleep-waking phases, and to obtain additional data about the participation of 5-HT2 receptors in the regulation of sleep and wake behaviour. Six sleep-waking stages were detected: active waking, quiet waking, light slow-wave sleep, deep slow-wave sleep, intermediate stage of sleep and paradoxical sleep. Each of the 12-h postdrug EEG records was divided into 3 consecutive 4-hour periods and the sleep-waking stages were scored visually for every minute of the whole postdrug period. The three periods were compared in order to evaluate the effect of ritanserin in dynamics. The results obtained showed a significant decrease in wakefulness and paradoxical sleep, a significant increase in slow-wave sleep (mainly the deep slow-wave sleep) and in the intermediate stage of sleep. These changes in the sleep-waking phases occurred in a dose-dependent manner, the larger the dose of ritanserin, the stronger the effect of ritanserin. The changes were more pronounced during the first 4-h period and then a restoration in the sleep-waking phases took place except for the paradoxical sleep.
DUSPs, to MAP kinases and beyond (2012)

Phosphatases are important regulators of intracellular signaling events, and their functions have been implicated in many biological processes. Dual-specificity phosphatases (DUSPs), whose family currently contains 25 members, are phosphatases that can dephosphorylate both tyrosine and serine/threonine residues of their substrates. The archetypical DUSP, DUSP1/MKP1, was initially discovered to regulate the activities of MAP kinases by dephosphorylating the TXY motif in the kinase domain. However, although DUSPs were discovered more than a decade ago, only in the past few years have their various functions begun to be described. DUSPs can be categorized based on the presence or absence of a MAP kinase-interacting domain into typical DUSPs and atypical DUSPs, respectively. In this review, we discuss the current understanding of how the activities of typical DUSPs are regulated and how typical DUSPs can regulate the functions of their targets. We also summarize recent findings from several in vivo DUSP-deficient mouse models that studied the involvement of DUSPs during the development and functioning of T cells. Finally, we discuss briefly the potential roles of DUSPs in the regulation of non-MAP kinase targets, as well as in the modulation of tumorigenesis.
Magnetic microrobots with addressable shape control (2016)

Shape shifting soft microrobots are generated from self-folding hydrogel bilayer structures. The folding conditions are analyzed to develop an optimal strategy for producing desired three-dimensional shapes. We present two different methods for programming magnetization in these microrobots that are variant and invariant to folding. The microrobots can be navigated through user-defined trajectories using rotating magnetic fields, and the morphing in response to temperature changes can be tuned for adaptive behavior. On-demand modulation of the mobility of individual microrobots is demonstrated by morphing their shape using selective near infrared light (NIR) exposure.
The Insall-Burstein posterior stabilized total knee replacement in the valgus knee. (1996)

Sixty-seven Insall-Burstein (Zimmer Inc, Warsaw, Indiana) posteriorly stabilized total knee replacements were implanted in knees with a preoperative alignment > 10 degrees of valgus (average: 19.5 degrees). An anteromedial approach with release of the lateral ligaments of the femur was used. A lateral patellar release was necessary in 49% of cases. Fifty-one knees (76%) were reviewed with an average follow-up of 6 years. Pain at follow-up was absent or mild in all of the knees except one with aseptic loosening of the tibial and patellar components. The average flexion was 105 degrees. The results according to the Knee Society Rating System were excellent in 53%, good in 39%, fair in 6%, and poor in 2%. A patellofemoral "clunk" was present in three knees (6%), and one knee required arthroscopic debridment. The mechanical axis was within 5 degrees of neutral in 88%. A survivorship analysis was performed using failure requiring reoperation as the end point. There were four failures due to aseptic loosening, symptomatic lateral ligamentous instability, deep infection, and recurrent patellar dislocation. The patellar component had not been implanted in the knee with recurrent patellar dislocation due to severe bony erosion. The cumulative success rate was 95% at 10 years. These results indicate that release of the contracted lateral structures and implantation of a posteriorly stabilized prosthesis achieve a stable and well-aligned knee in 66 out of 67 knees. Attention must be paid to patellar tracking and realignment of the extensor mechanism.
An algorithm for automated fuzzy logic controller tuning (2003)

An automated method for calibrating a fuzzy logic controller (FLC) has been developed based on the cell state-space concept. The system's state space is quantized into cells creating a spatially discrete model of system behavior. Given a cost function and plant simulation model, a cell-state-space-based optimal control algorithm generates a table of desired control actions. The control table provides a discrete approximation to the global optimal control policy with respect to the cost function. An adjusted cost function algorithm is presented that uses fuzzy constraints to improve the accuracy of the control table. In addition, a nonuniform quantization scheme is described that also improves the accuracy of both the control table and the cell mappings used for analysis. The performance and robustness characteristics of an FLC designed using this automated method were explored with the minimum time control of an inverted pendulum.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Expression and Purification of Glutathione‐<i>S</i>‐Transferase Fusion Proteins (1994)

This unit describes how pGEX vectors can be used in bacterial systems to express foreign polypeptides as fusions with glutathione-S-transferase (GST). In general, such fusion proteins are soluble and are easily purified from lysed cells under nondenaturing conditions by absorption with glutathione-agarose beads, followed by elution in the presence of free glutathione. Potential applications of the pGEX vectors include the expression and purification of individual polypeptides (including short peptides) for use as immunogens and as biochemical and biological reagents, and in the construction of cDNA expression libraries. This protocol describes production and screening of pGEX transformants and purification of milligram quantities of fusion proteins from 1-liter cultures. The commentary describes several modifications to the expression and purification protocol that may be useful in cases where fusion proteins are insoluble or unstable.
A Low Complexity PMI/RI Selection Scheme in LTE-A Systems (2013)

Recent wireless radio technologies have utilized precoding matrix and rank adaptation as a technique to increase frequency efficiency. In 3rd generation partnership project (3GPP) long term evolution (LTE) and LTE-advanced (LTE-A) systems, codebook based precoding is utilized. In the codebook based system, a mobile station (MS) needs to estimate optimum channel state information (CSI) which includes a channel quality indicator (CQI), a precoding matrix indicator (PMI) and rank indicator (RI) and to feed back the CSI to the base station (BS) in order to get higher frequency efficiency. Generally, the MS estimates the optimum precoding matrix from all possible precoding matrices which are predefined as the codebook. When such an exhaustive search algorithm is utilized in LTE-A MS, the MS needs huge computation power because the number of rank and precoding matrix patterns is large in a LTE-A system. In this paper, we propose a novel PMI/RI selection algorithm which is less complex than the exhaustive search algorithm in a LTE-A system. After evaluating the throughput performances by simulation and analyzing the computations, it is described that the proposed algorithm has the same throughput performances as the conventional algorithm and 13% of the computations compared with the conventional algorithm.
Amino acid sequence determination of Ancrod, the thrombin‐like α‐fibrinogenase from the venom of <i>Akistrodon rhodostoma</i> (1992)

The thrombin-like serine protease and antithrombotic agent, Ancrod, was rapidly purified from the crude venom of Akistrodon rhodostoma by agmatine-Sepharose affinity chromatography followed by MonoQ anion exchange chromatography. N-Terminal sequencing and analysis of overlapping proteolytic fragments of purified Ancrod by automated Edman degradation in combination with tandem mass spectroscopy allowed the determination of the 234 amino acid sequence of the protease. Glycosylation sites at all five canonical N-linked glycosylation sites were inferred from the appearance of blank sequencer cycles in the amino acid sequence and were confirmed by mass spectroscopic analysis of the N-glycanase-treated peptides. Monoclonal antibodies raised against the denatured protein and HF-deglycosylated protein recognized Ancrod on Western blots. Sequence comparison to other thrombin-like serine proteases and reptilian fibrinogenases revealed a number of similarities, most notably the catalytic triad and many conserved cysteine positions.
Comparisons of Sculpting Efficiency Between Mudbox and ZBrush (2012)

It is difficult to navigate throughout todays existing sculpting and modeling software. Industry drives the development in this area by “time versus quality.” It is difficult to know which software is the most suitable to learn for sculpting details, as well as which one is the most efficient for beginners. There are two software programs, Autodesk Mudbox and Pixologic ZBrush, which will be examined and reviewed for sculpting details, learning curve for beginners, and time efficiency in this research. The overall results displayed that ZBrush seems to be the better choice for more advanced modellers and artists, while Mudbox is a better choice for beginners and more technical modellers.
Loop-level parallelism in numeric and symbolic programs (1993)

A new technique for estimating and understanding the speed improvement that can result from executing a program on a parallel computer is described. The technique requires no additional programming and minimal effort by a program's author. The analysis begins by tracing a sequential program. A parallelism analyzer uses information from the trace to simulate parallel execution of the program. In addition to predicting parallel performance, the parallelism analyzer measures many aspects of a program's dynamic behavior. Measurements of six substantial programs are presented. These results indicate that the three symbolic programs differ substantially from the numeric programs and, as a consequence, cannot be automatically parallelized with the same compilation techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Rotor Track and Balance Improvements (2013)

   Vibration derived from the main rotor dynamics and imbalance causes premature wear to the aircraft components, and can cause pilot fatigue. While improvements have been made in rotor track and balance (RTB) techniques; there is room to enhance the quality of the recommended RTB adjustments. One aspect that limits the development of RTB algorithms is the difficulty in quantifying the performance of new algorithms. This is because there are limited data sets to work on, and no agreed upon metrics on which to measure RTB performance.This paper develops a methodology to simulate the vibration due to injecting a fault into the rotor system, and demonstrates metrics to evaluate the performance of a RTB algorithm. A new Bayes RTB method is evaluated against a standard least squares technique. In addition, a technique is presented to automate the selection of active adjustments.
Injectable <i>In Situ</i> –Forming pH/Thermo-Sensitive Hydrogel for Bone Tissue Engineering (2008)

We developed a novel pH- and thermo-sensitive hydrogel as a scaffold for autologous bone tissue engineering. We synthesized this polymer by adding pH-sensitive sulfamethazine oligomers (SMOs) to both ends of a thermo-sensitive poly(epsilon-caprolactone-co-lactide)-poly(ethylene glycol)-poly(epsilon-caprolactone-co-lactide) (PCLA-PEG-PCLA) block copolymer, yielding a pH/thermo-sensitive SMO-PCLA-PEG-PCLA-SMO block copolymer. The synthesized block copolymer solution rapidly formed a stable gel under physiological conditions (pH 7.4 and 37 degrees C), whereas it formed a sol at pH 8.0 and 37 degrees C, making it injectable. This pH/thermo-sensitive hydrogel exhibited high biocompatibility in a Dulbecco's modified Eagle's medium extract test. Under physiological conditions, the hydrogel easily encapsulated human mesenchymal stem cells (hMSCs) and recombinant human bone morphogenetic protein-2 (rhBMP-2), with encapsulating efficiencies of about 90% and 85%, respectively. To assay for ectopic bone formation in vivo, we subcutaneously injected a polymer solution containing hMSCs and rhBMP-2 into the back of mice, after which we could observe hMSC differentiation for up to 7 weeks. Histological studies revealed mineralized tissue formation and high levels of alkaline phosphatase activity in the mineralized tissue. Therefore, this pH/thermo-sensitive SMO-PCLA-PEG-PCLA-SMO block copolymer demonstrated potential as an injectable scaffold for bone tissue engineering, with in situ formation capabilities.
The <i>rfaE</i> Gene from <i>Escherichia coli</i> Encodes a Bifunctional Protein Involved in Biosynthesis of the Lipopolysaccharide Core Precursor ADP- <scp>l</scp> - <i>glycero</i> - <scp>d</scp> - <i>manno</i> -Heptose (2000)

ABSTRACT The intermediate steps in the biosynthesis of the ADP- l - glycero - d - manno -heptose precursor of inner core lipopolysaccharide (LPS) are not yet elucidated. We isolated a mini-Tn 10 insertion that confers a heptoseless LPS phenotype in the chromosome of Escherichia coli K-12. The mutation was in a gene homologous to the previously reported rfaE gene from Haemophilus influenzae . The E. coli rfaE gene was cloned into an expression vector, and an in vitro transcription-translation experiment revealed a polypeptide of approximately 55 kDa in mass. Comparisons of the predicted amino acid sequence with other proteins in the database showed the presence of two clearly separate domains. Domain I (amino acids 1 to 318) shared structural features with members of the ribokinase family, while Domain II (amino acids 344 to 477) had conserved features of the cytidylyltransferase superfamily that includes the aut gene product of Ralstonia eutrophus . Each domain was expressed individually, demonstrating that only Domain I could complement the rfaE ::Tn 10 mutation in E. coli , as well as the rfaE543 mutation of Salmonella enterica SL1102. DNA sequencing of the rfaE543 gene revealed that Domain I had one amino acid substitution and a 12-bp in-frame deletion resulting in the loss of four amino acids, while Domain II remained intact. We also demonstrated that the aut ::Tn 5 mutation in R. eutrophus is associated with heptoseless LPS, and this phenotype was restored following the introduction of a plasmid expressing the E. coli Domain II. Thus, both domains of rfaE are functionally different and genetically separable confirming that the encoded protein is bifunctional. We propose that Domain I is involved in the synthesis of d - glycero - d - manno -heptose 1-phosphate, whereas Domain II catalyzes the ADP transfer to form ADP- d - glycero - d - manno -heptose.
Profiling Database Application to Detect SQL Injection Attacks (2007)

Countering threats to an organization's internal databases from database applications is an important area of research. In this paper, we propose a novel framework based on anomaly detection techniques, to detect malicious behaviour of database application programs. Specifically, we create a fingerprint of an application program based on SQL queries submitted by it to a database. We then use association rule mining techniques on this fingerprint to extract useful rules. These rules succinctly represent the normal behaviour of the database application. We then apply an anomaly detection algorithm to detect queries that do not conform to these rules. We further demonstrate how this model can be used to detect SQL Injection attacks on databases. We show the validity and usefulness of our approach on synthetically generated datasets and SQL Injected queries. Experimental results show that our techniques are effective in addressing various types of SQL Injection threat scenarios.
The acute cognitive effects of zopiclone, zolpidem, zaleplon, and eszopiclone: A systematic review and meta-analysis (2014)

The "z-drugs" zopiclone, zolpidem, eszopiclone, and zaleplon were introduced in the 1980s for the treatment of insomnia, as it was observed that the side effect profile associated with these medications were more benign than those related to the benzodiazepines. This meta-analysis set out to ascertain which domains of cognitive function, if any, were affected by the ingestion of these medications. A total of 20 studies met the study inclusion criteria. Results revealed medium effect sizes for zopiclone and zolpidem on measures of verbal memory. An additional medium effect size was observed for zolpidem on attention. Finally, smaller effect sizes were observed for zolpidem speed of processing and for zopiclone on working memory. It is clear from these data that the use of a single dose of the z-drugs in healthy adults as measured in the morning following the exposure does produce a specific rather than a generalized negative effect on cognitive function. However, there were only enough studies to evaluate the individual cognitive effects of the zolpidem and zopiclone medications; the specific effects of zaleplon and eszopiclone cannot be ascertained because only one study met the inclusion and exclusion criteria for the review.
A 10-bit Low-Power Small-Area High-Swing CMOS DAC (2010)

The design and measurements of a prototype general purpose digital to analog converter for readout systems in high energy physics experiments are presented. The main goals for the proposed DAC are low power consumption, small die area and high-swing voltage output. The 10-bit DAC design is based on a current steering architecture which includes a high-swing class AB output amplifier. The prototype ASIC is fabricated using 2P-4M 0.35- ¿m technology. Measurements of maximum differential (DNL) and integral (INL) nonlinearity both show 0.42 LSB. The total power consumption is below 0.6 mW while the core area is 0.18 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .