gebhart/patrepeval huggingface dataset:
CRISPR Gene Therapy: Applications, Limitations, and Implications for the Future (2020)

A series of recent discoveries harnessing the adaptive immune system of prokaryotes to perform targeted genome editing is having a transformative influence across the biological sciences. The discovery of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins has expanded the applications of genetic research in thousands of laboratories across the globe and is redefining our approach to gene therapy. Traditional gene therapy has raised some concerns, as its reliance on viral vector delivery of therapeutic transgenes can cause both insertional oncogenesis and immunogenic toxicity. While viral vectors remain a key delivery vehicle, CRISPR technology provides a relatively simple and efficient alternative for site-specific gene editing, obliviating some concerns raised by traditional gene therapy. Although it has apparent advantages, CRISPR/Cas9 brings its own set of limitations which must be addressed for safe and efficient clinical translation. This review focuses on the evolution of gene therapy and the role of CRISPR in shifting the gene therapy paradigm. We review the emerging data of recent gene therapy trials and consider the best strategy to move forward with this powerful but still relatively new technology.
Carbon Fiber Morphology. 2. Expanded Wide-Angle X-Ray Diffraction Studies of Carbon Fibers (1991)

Abstract : This report, describes the wide-angle x-ray diffraction studies and results on carbon and graphite fibers. Commercial PAN- and pitch-based carbon fibers spanning the generally available modulus range were examined. Crystal perfection, size, orientation, and degree of graphitization and calculated voids content are correlated with tensile modulus, tensile strength, and compression strength. These same parameters are examined as a function of heat treatment of several fibers as well.
Microwear in Modern Rooting and Stall-fed Pigs: the Potential of Dental Microwear Analysis for Exploring Pig Diet and Management in the Past (1999)

In recent years dental microwear analysis has attracted considerable interest as a potential method for reconstructing ancient diet. The potential of dental microwear for reconstructing pig diet and management within an archaeological context is explored through the analysis of microwear patterning in modern stall-fed and free-range/rooting pigs. Stall-fed pigs are readily distinguished from rooting/free-range pigs by the greater density of microwear features evident in the latter on both buccal and occlusal surfaces. This distinction can be attributed to the more abrasive diet of the free-ranging pigs, as a consequence of soil ingestion during rooting.
Persistent-mode operation of a cryocooler-cooled HTS magnet (2002)

Persistent-mode operations of a cryocooler-cooled HTS magnet were carried out. The closed circuit of the magnet consisted of a Bi-2212 solenoid coil and a NbTi/CuNi persistent-current switch (PCS). Thermal conductance between the PCS and the cooling stage was designed not to heat up the coil. The temperature increase was maintained within 0.1 K during the normal state of the PCS. The transition times of the PCS between a superconducting and a normal state were sufficiently short for practical use. The magnet started a persistent-mode operation from an initial magnetic field of 2.1 T. Decay behaviors during persistent-mode operations were successfully observed over 90 hours. Except for the initial period, field decay was limited by resistance of the joint. A method to compensate the field decay was performed by installing a NbTi cylinder in the coil bore.
Fiber-optic evanescent field absorption sensor (1987)

Waveguide evanescent field absorption has been measured as a function of cladding refractive index and bulk absorption coefficient. A simple theory for interpreting these results has been developed. An all-fiber species concentration sensor has been constructed and its performance characterized.
Quantification of Neuroreceptors in the Living Human Brain: IV. Effect of Aging and Elevations of D<sub>2</sub>-Like Receptors in Schizophrenia and Bipolar Illness (1997)

In a previous study of 10 drug-naive schizophrenic patients, the density of D2 dopamine receptors was found to be elevated in the caudate nucleus. The study raised questions about the influence of the age of the patients, the relationship of receptor density to psychosis, and the accuracy of the method used to obtain this evidence. Using positron emission tomography and constrained analysis of the brain uptake of the radioligand N-[11C]methyl-spiperone ([11C]NMSP), we tested four questions: Were the assumptions underlying the quantitation valid? Is there an age decline of the density of D2-like dopamine receptors in drug-naive schizophrenia and bipolar illness? If so, is it different from that observed in normal aging? Are D2-like dopamine receptors elevated at any age in either drug-naive schizophrenic or psychotic bipolar illness patients? NMSP and haloperidol partition volumes and plasma protein fractions were not significantly different among patient groups and normal volunteers. The model-derived assay of radioligand metabolites in plasma was confirmed by high-performance liquid chromatography in the patient groups. D2-like dopamine receptors declined with age, and the slope did not differ significantly between the schizophrenic patients, bipolar affective illness patients, and normal controls. Taking the effect of age into account, increases in D2 dopamine receptor density were found in seven psychotic patients with bipolar affective illness compared with seven nonpsychotic patients and 24 control subjects as well as in 22 drug-naive schizophrenic patients compared with the 24 control subjects.
The Damaging Effect of Passenger Mutations on Cancer Progression (2017)

Genomic instability and high mutation rates cause cancer to acquire numerous mutations and chromosomal alterations during its somatic evolution; most are termed passengers because they do not confer cancer phenotypes. Evolutionary simulations and cancer genomic studies suggest that mildly deleterious passengers accumulate and can collectively slow cancer progression. Clinical data also suggest an association between passenger load and response to therapeutics, yet no causal link between the effects of passengers and cancer progression has been established. To assess this, we introduced increasing passenger loads into human cell lines and immunocompromised mouse models. We found that passengers dramatically reduced proliferative fitness (∼3% per Mb), slowed tumor growth, and reduced metastatic progression. We developed new genomic measures of damaging passenger load that can accurately predict the fitness costs of passengers in cell lines and in human breast cancers. We conclude that genomic instability and an elevated load of DNA alterations in cancer is a double-edged sword: it accelerates the accumulation of adaptive drivers, but incurs a harmful passenger load that can outweigh driver benefit. The effects of passenger alterations on cancer fitness were unrelated to enhanced immunity, as our tests were performed either in cell culture or in immunocompromised animals. Our findings refute traditional paradigms of passengers as neutral events, suggesting that passenger load reduces the fitness of cancer cells and slows or prevents progression of both primary and metastatic disease. The antitumor effects of chemotherapies can in part be due to the induction of genomic instability and increased passenger load. <i>Cancer Res; 77(18); 4763-72. ©2017 AACR</i>.
Spherical fibonacci mapping (2015)

Spherical Fibonacci point sets yield nearly uniform point distributions on the unit sphere S 2 ⊂ R 3 . The forward generation of these point sets has been widely researched and is easy to implement, such that they have been used in various applications. Unfortunately, the lack of an efficient mapping from points on the unit sphere to their closest spherical Fibonacci point set neighbors rendered them impractical for a wide range of applications, especially in computer graphics. Therefore, we introduce an inverse mapping from points on the unit sphere which yields the nearest neighbor in an arbitrarily sized spherical Fibonacci point set in constant time, without requiring any precomputations or table lookups. We show how to implement this inverse mapping on GPUs while addressing arising floating point precision problems. Further, we demonstrate the use of this mapping and its variants, and show how to apply it to fast unit vector quantization. Finally, we illustrate the means by which to modify this inverse mapping for texture mapping with smooth filter kernels and showcase its use in the field of procedural modeling.
Effect of 2'-deoxyisoguanosine on the growth of human tumor and normal cell lines. (2004)

2'-deoxyisoguanosine has low potency and specificity in inhibiting tumor cell growth, similar to other telomerase inhibitors.
<i>nab</i> -Paclitaxel Potentiates Gemcitabine Activity by Reducing Cytidine Deaminase Levels in a Mouse Model of Pancreatic Cancer (2012)

This study provides mechanistic insight into the clinical cooperation observed between gemcitabine and nab-paclitaxel in the treatment of pancreatic cancer.
Utility of Baroreflex Sensitivity as a Marker of Stress (2016)

Presently, adaptive systems use various cognitive and cardiovascular measures to evaluate the functional state of the operator. One marker that has been largely ignored as an assessment tool is baroreflex sensitivity (BRS). This study examined the extent to which BRS changed in response to acute psychological and physical stressors. A total of 20 participants underwent 6-min exposures to a psychological stressor and a physical stressor. Baroreceptor sensitivity, blood pressure, heart rate, heart rate variability, stroke volume, cardiac output, mean blood pressure, total peripheral resistance, left ventricular ejection time, and pre-ejection period were continuously measured at rest and throughout the testing period. Compared to rest, BRS significantly decreased during both the psychological and physical stressors. BRS was reduced more with the psychological stressor than the physical stressor. Heart rate and systolic blood pressure significantly increased above rest during the psychological stressor but not during the physical stressor. There were no significant differences from rest or between stressors for the other physiological markers. BRS was more robustly responsive than other cardiovascular measures commonly used to assess the psychophysiological response to stress, suggesting BRS is a useful marker for evaluating operator functional state during psychological and physical tasks.
PVF<inf>2</inf>Polymer Microprobe (1979)

This paper describes the design and performance of a PVF2 microprobe for use in mapping the pressure field from arrays. For medical applications, the probe must have short pulse response (i.e., broad, flat bandwidth) in addition to high sensitivity, low noise, and a wide acceptance angle. The factors that influence critical parameters, such as ringing and delayed reverberations, are specifically discussed. The probe has a center frequency of about 3 MHz. It consists of a 1.5 mm diameter disc of PVFZ polymer (30 pm thick) operated well below its resonance to obtain very broad frequency response. The PVFz is completely encased in a metal cylinder to shield it from spurious electromagnetic interference and to protect the polymer from possible corrosion by external fluids. An FET amplifier is integral to the probe housing. The experimental performance of the probe is compared with theoretical predictions, acoustically and electrically. It is also compared with the performance of other probes, including a laser pellicle system, for pulse fidelity and signal-to-noise ratio.
Two-Photon Excitation Laser Scanning Microscopy of Human, Porcine, and Rabbit Nasal Septal Cartilage (2001)

Two-photon excitation laser scanning microscopy (TPM) was used to image human, porcine, and rabbit nasal septal cartilage. TPM provides optical sections of thick tissue specimens in situ without the use of exogenous dyes or need for tissue fixation. The cartilage tissue was imaged using near-infrared light generated by a mode-locked titanium/sapphire laser that was raster-scanned and coupled to an inverted microscope. Absorption of two photons by endogenous molecules and subsequent fluorescence was filtered to specific spectral bandwidths and detected with photomultiplier tubes. Two-photon stimulated fluorescence was detected with photomultiplier tubes optimized to specific spectral bandwidths. Signal intensity corresponds to the concentration of fluorophores, principally NADH, NADPH, and flavoproteins hence providing a means of redox imaging the cellular metabolic state. Specimens were scanned from the surface to a depth of about 150 microm. Image size was 50 x 50 microm with a diffraction limited pixel size of 0.4 microm. Cell membranes, nuclei, and matrix structures were identified in human, pig, and rabbit tissues. TPM provides a means to study three dimensional chondrocyte structure and matrix organization in situ at substantial depths, and permits longitudinal examination of cultured tissue explants without the need for exogenous dyes, tissue preparation, or fixation.
Natural Killer Cell Cytotoxicity: A Methods Analysis of Versus Flow Cytometry Chromium Release (2003)

The purpose of this study is to describe design considerations for the use of flow cytometry (FC) compared to 51chromium (51Cr)-release assays utilizing cryopreserved peripheral blood mononuclear cells (PBMCs) to detect natural killer (NK) cell cytotoxicity. Subjects were 10 healthy women aged 18 to 39 years. Intra-assay variability between methods differed only at the lowest effector-target ratios evaluated. Interassay variability was wide but did not differ between methods. The relationship of lytic unit-10 between methods was strongly positive. Cytotoxicity detected by 51Cr release was higher than that detected by FC for all 10 subjects. Cost was comparable. However, had more assays been performed, technician time would have been greater with flow cytometry. More whole blood was needed to perform the flow cytometry cytotoxicity assay than 51Cr-release cytotoxicity assay. The authors found no compelling reason to adopt NK cell cytotoxicity by flow cytometry over 51Cr release.
Chemical composition of ferrierite (1976)

Ferrierite specimens from localities at Altoona, Washington; Silver Mountain, Alpine County, California; and Pinaus Lake, Monte Lake, and Francois Lake, British Columbia, have been analyzed by microprobe methods. These new analyses are combined with available data to delineate the compositional range for this zeolite. The frame work composition ranges from (Al7 •5Si27 5072) to (Al ,Si a,072). The a cell dimension varies linearly with the Si content. There are between 3 and 5 exchangeable cations (univalent and divalent) per unit cell of 72 oxygens, but with wide variations; the amount of univale11t ions ranges from 21 to 85 percent. There is no clear parititioning of the univalent ions, as the Na/(Na+K) ratio is highly variable. Mg is clearly fractionated in all ferrierites (Ca/(Ca + Mg) < 0.40), regardless of the amount of divalent ions. The highest known amounts of BaO (2.54%) and SrO (0.40%) are in the Silver Mountain ferrierite. Associated zeolites commonly include clinoptilolite or heulandite, although mordenite and dachiardite also occur with ferrierite at Altoona. The broad compositional range of ferrierite indicates that it can crystallize from solutions with a wide variety of alkali and alkaline earth cations, none of which are essential to the zeolite. If present, Mg ions are fractionated into the zeolite. Ferrierite crystallizes in response to high silica activities. However, to account for the range in silica contents, the a810, must be coupled with other variables, such as temperature or aH,o, in order to prevent crystallization
An airport cargo inspection system based on X-ray and thermal neutron analysis (TNA) (2005)

A cargo inspection system incorporating a high-resolution X-ray imaging system with a material-specific detection system based on Ancore Corporation's patented thermal neutron analysis (TNA) technology can detect bulk quantities of explosives and drugs concealed in trucks or cargo containers. The TNA process utilises a 252Cf neutron source surrounded by a moderator. The neutron interactions with the inspected object result in strong and unique gamma-ray signals from nitrogen, which is a key ingredient in modern high explosives, and from chlorinated drugs. The TNA computer analyses the gamma-ray signals and automatically determines the presence of explosives or drugs. The radiation source terms and shielding design of the facility are described. For the X-ray generator, the primary beam, leakage radiation, and scattered primary and leakage radiation were considered. For the TNA, the primary neutrons and tunnel scattered neutrons as well as the neutron-capture gamma rays were considered.
ALBERT---Software for scientific computations and applications. (2001)

Abstract. Adaptive finite element methods are a modern, widely used tool which make realistic computations feasible, even in three space dimensions. We describe the basic ideas and ingredients of adaptive FEM and the implementation of our toolbox ALBERT. The design of ALBERT is based on the natural hierarchy of locally refined meshes and an abstract concept of general finite element spaces. As a result, dimension independent programming of applications is possible. Numerical results from applications in two and three space dimensions demonstrate the flexibility of ALBERT. ALBERT
Radioiodination and biological distribution of a new <i>s</i>‐triazine derivative for tumor uptake evaluation (2018)

A newly synthesized s-triazine derivative 1,1',1″-(((1,3,5-triazine-2,4,6-triyl) tris (azanediyl)) tris (benzene-4,1-diyl))tris (ethan-1-one), (1), was synthesized as a part of an ongoing research for development of novel s-triazine-based radiopharmaceuticals. In-vitro cell viability assay against different human cancer cell lines showed very promising inhibitory activity of the synthesized compound. This finding encouraged the radioiodination of 1 to study the degree of its localization in tumor site for evaluating the possibility of its use as a tumor imaging agent. The biodistribution study showed good localization of the radioiodinated derivative 2 at tumor site following i.v. administration in solid tumor-bearing mice. Finally, in a trial to understand the mechanism of the anticancer effect exerted by 1, a target prediction study and a docking study were performed. The results of the first study showed that focal adhesion kinase is a possible target for compound 1 and the docking study confirmed successful binding of both compound 1 and its radioiodinated derivative 2 to the binding site of focal adhesion kinase. As a conclusion, the results of this study suggest that, compound 2 could be used as a potential agent for tumor imaging after preclinical trials.
High Levels of Aberrant DNA Methylation in <i>Helicobacter pylori</i> –Infected Gastric Mucosae and its Possible Association with Gastric Cancer Risk (2006)

It was indicated that H. pylori infection potently induces methylation of CGIs to various degrees. Methylation levels of specific CGIs seemed to reflect gastric cancer risk in H. pylori-negative individuals.
Low avidity IgG antibodies in diagnosis of recent human schistosomiasis. (2002)

One hundred thirty school children from a schistosomiasis endemic area in Sharkia Governorate, were selected on parasitological findings. Seventy persons were negative on the first screen and turned positive after 3 months of the screening (recently infected). Stool examination, ELISA (IgG & IgM), low avid IgG, and circulating antigens were performed for all patients and controls. ELISA detected IgM in all cases. IgG and circulating antigens in 90% of schistosomiasis patients. Low avidity IgG were detected in 85.71% of recent cases. The specificity of ELISA appeared to be >99%. The IgM/IgG ratio was >1 in patients with recent infection. The percentage of fall of O.D. readings of IgG after addition of 6 molar urea was high among cases with recent infection. Low avid lgG appears to be good and valuable in diagnosis of recent schistosomiasis in man.
Non-peptide guided auto-secretion of recombinant proteins by super-folder green fluorescent protein in Escherichia coli (2017)

Protein secretion in Escherichia coli is usually led by a signal peptide that targets the protein to specific secretory pathways. In this study, we demonstrated that the superfolder green fluorescent protein (sfGFP) could be served as a non-signal peptide to guide protein auto-secretion in E. coli. This auto-secretion was characterized as a three-step process through the sub-cellular localization analysis: inner membrane trans-location followed by anchoring at outer membrane, and then being released into culture media. We further determined that the beta-barrel structure and net negative charges of sfGFP played important roles in its auto-extracellular secretion property. Using sfGFP as a carrier, heterologous proteins ranging from peptide to complex protein, including antibacterial peptide PG4, endo-beta-N-acethylglucosamindase H (Endo H), human arginase-1 (ARG1), and glutamate decarboxylase (GAD) were all successfully expressed and secreted extracellularly when fused to the carboxyl end of sfGFP. Besides facilitating the extracellular secretion, sfGFP fusion proteins can also be correctly folded and formed the active complex protein structure, including the trimetric human ARG1 and homo-hexametric GAD. This is the first report that sfGFP can guide the secretion of recombinant proteins out of the cells from cytoplasm in E. coli without affecting their conformation and function.
Culture of chicken embryos in surrogate eggshells (2005)

The chick embryo is a classical model to study embryonic development. However, most researchers have not studied the effect of embryonic manipulation on chick hatchability. The objective of this study was to determine the effect of egg orientation and type of sealing film on the hatchability of cultured embryos. Windows were made in the small end of recipient surrogate chicken eggshells, and donor embryos were placed into the recipient eggshell for the first 3 d of incubation. Survival over the first 3 d was maximized (P < 0.05) when windowed eggs sealed with Saran Wrap were positioned with the window-end down compared with window-end up. Three-day-old cultured embryos were transferred into recipient turkey eggshells, sealed with cling film, and cultured until hatch. Water weight loss of the surrogate eggshell cultures regardless of cling film type was not significantly different from control intact eggs. The embryos cultured in turkey eggshells and sealed with Handi Wrap exhibited higher hatchability (75% +/- 10.2%) than cultures sealed with Saran Wrap (45.2% +/- 13.8%). Hatchability of control intact eggs (86.4% +/- 5.3%) was not significantly (P > 0.05) different from the hatchability of eggs sealed with Handi Wrap, which suggested that Handi Wrap was an excellent sealant for chick embryos cultured after 3 d of incubation.