gebhart/patrepeval huggingface dataset:
Noninvasive prenatal detection of sex chromosomal aneuploidies by sequencing circulating cell‐free DNA from maternal plasma (2013)

Noninvasive prenatal identification of the most common sex chromosome aneuploidies is possible using ccf DNA and massively parallel sequencing with a high DR and a low FPR.
Synthesis of Levoglucosenone (1990)

Abstract Levoglucosenone was synthesized from D-galactose via reductive decarboxylation as a key reaction. Among the catalysts used for the key reaction, hydrous zirconium oxide was found to have the best activity.
<i>β</i> -Galactosidase Gene Transfer to Human Malignant Glioma <i>In Vivo</i> Using Replication-Deficient Retroviruses and Adenoviruses (1998)

Both retro- and adenovirus-mediated gene therapy have been suggested as a novel approach to the treatment of malignant brain tumors. However, little information is available about the gene transfer efficiency in human malignant glioma in vivo. We compared the feasibility and safety of retrovirus- and adenovirus-mediated beta-galactosidase gene transfer in human malignant glioma. Beta-galactosidase gene was transferred to 10 patients with malignant glioma via a catheter inserted into the tumor. The catheter was left in place until the tumor resection. To maximize gene transfer efficiency, gene transfer vectors (BAG retroviruses, titer, 6 x 10(5) CFU; and adenoviruses, titer from 3 x 10(8) to 3 x 10(10) PFU) were injected into the tumor via the catheter once a day for three consecutive days, followed by tumor resection 1-2 days later. Tumor was resected in such a way that the catheter was still in place inside the tumor, which permitted accurate histological analysis of the transduced tumors. X-Gal staining for beta-galactosidase activity was used to study gene transfer efficiency and distribution of the marker gene. Beta-galactosidase gene transfer was well tolerated with both vectors. Except for two patients with clear increases in serum adenovirus antibody titers, no adverse tissue responses or systemic complications were noticed in any of the patients. Gene transfer was successful in all patients. Gene transfer efficiency varied between <0.01 and 4% with retroviruses and between <0.01 and 11% with adenoviruses. However, the transgene activity was not evenly distributed in the tumors. Both glioma cells and endothelium in the tumor blood vessels were transduced with retro- and adenovirus vectors. In conclusion, the safety and feasibility of in vivo gene transfer to human malignant glioma was established with retro- and adenovirus vectors. Adenoviruses were more efficient than retroviruses in achieving in vivo gene transfer. Transduction of endothelial cells may have important consequences for the proposed treatment strategies and selection of treatment genes. The results justify clinical gene therapy trials for malignant glioma.
Quantifying locality (1993)

A direct measure of the locality characteristics of reference streams is presented that quantifies the concepts of locality. The new locality definition unifies the traditional concepts of temporal and spatial locality and represents the probability that the first occurrence of an access to a memory location a distance of s away from the current location occurs within the next $1\over 2$d to d references. The locality definition has useful properties that allow insight to be gained into the trace structures that correspond to various locality features.
The locality of reference streams is shown to be a meaningful metric by which the interaction of reference streams and locality dependent subsystems can be quantified and visualized. Applications of this technique explored in this work include trace characterization, algorithm classification, cache parameter estimation, workload profiling, benchmark evaluation, and reference model evaluation. An examination of the locality characteristics at each level in the memory hierarchy reveals that the locality characteristics of reference streams account for the general architecture and design decisions common at each level.
The locality characteristics of the UNIX SVR4 monolithic operating system and MACH 3.0 microkernel operating system are contrasted. Also, the differences in locality between references generated by the SPARC RISC processor and the i486 CISC processor are quantified.
Single-cell photonic nanocavity probes (2014)

The use of nanometer-sized probes for single-cell studies is presented by Gary Shambat of Adamant Technologies (USA) in, "Single-cell Photonic Nanocavity Probes." This work, conducted by Shambat at Stanford University in Jelena Vukovic's lab, seeks to extend traditional nanoprobe work by being able to insert a nanobeam into a single cell without damaging the cell. By functionalizing the beam, the team enables single-cell studies, essentially taking the lab to the biological system instead of extracting the biological system for study in a lab. The probe consists of a nanobeam optical cavity resulting from the tapering a GaAs device containing InAs quantum dots and coupled to an optical fiber to enable handling. The team demonstrated the ability to insert and retract the beam from PC3 cells (prostate cancer cells) in a reversible and elastic fashion. Using this technique allowed a study of the optical properties of the cell. Cell viability in this initial work was 75%. Future work includes in vitro protein sensing and adapting chemistries for studies of intracellular targets such as proteins, all of which may find applications in fields such as drug screening.
Expanding Acquisition and Clutter Filter Dimensions for Improved Perfusion Sensitivity (2017)

A method is explored for increasing the sensitivity of power-Doppler imaging without contrast enhancement. We acquire 1-10 s of echo signals and arrange it into a 3-D spatiotemporal data array. An eigenfilter developed to preserve all three dimensions of the array yields power estimates for blood flow and perfusion that are well separated from tissue clutter. This method is applied at high frequency (24-MHz pulses) to a murine model of an ischemic hindlimb. We demonstrate enhancements to tissue perfusion maps in normal and ischemic tissues. The method can be applied to data from any ultrasonic instrument that provides beamformed RF echo data.
Efficient Constitutive Production of Human IFN-γ in Chinese Hamster Ovary Cells (1986)

A human genomic DNA segment of 5.6 kb containing the entire gene for immune interferon-gamma was fused through its 5'-untranslated region to the corresponding region of the simian virus 40 (SV40) T-antigen gene. The SV40 early promoter used contained a modified transcriptional enhancer element with a 93-bp repeat. Supercoiled plasmid DNA was used to transfect Chinese hamster ovary (CHO) cells, the selectable marker being a SV40-dihydrofolate gene construct. Constitutive expression of the IFN-gamma gene in primary transformants was high, especially if a Harvey murine sarcoma virus long terminal repeat (LTR) was present in addition to the SV40 promoter. After gene amplification by methotrexate selection, CHO-gamma cell lines were obtained that produce 1.5-2 million units of IFN-gamma per million cells and per day (200,000 molecules per cell per minute). Metabolic labeling showed that over 90% of the protein secreted by such cells is human IFN-gamma. A one-step immuno-affinity chromatography on monoclonal antibodies yielded pure IFN-gamma with 1-2 X 10(8) units/mg protein. Like IFN-gamma from human white blood cells, the IFN-gamma from CHO-gamma cells is a mixture of two glycoproteins of 26,000 and 20,000 daltons with traces of the unglycosylated 17,000-dalton polypeptide. Large-scale cultures in 1% serum routinely yield over 600,000 units of human IFN-gamma/ml culture per day.
Kaposi's Sarcoma-Associated Herpesvirus and Kaposi's Sarcoma in Africa (1996)

<h3>Background:</h3> Endemic Kaposi's sarcoma (KS) is a clinically and epidemiologically distinct human immunodeficiency virus negative form of KS occurring in Africa. Kaposi's sarcoma is now the most frequently reported cancer in some areas of Africa. <h3>Objective:</h3> To determine if a KS-associated herpes-virus (KSHV) is present in both endemic HIV-seronegative and HIV-seropositive KS lesions from African patients. <h3>Methods:</h3> Paraffin-embedded tissue specimens from Ugandan patients with KS and non-KS tumor control patients attending a university-based oncology clinic were examined in a blinded case-control study. Tissue DNA specimens were examined for detectable KSHV genome by nested polymerase chain reaction performed at two independent laboratories. <h3>Results:</h3> We identified KSHV in 17 (85%) of 20 KS tissue specimens from HIV-seronegative patients and 22 (92%) of 24 KS tissue specimens from HIV-infected persons. Kaposi's sarcoma lesions from four HIV-infected persons and four HIV-seronegative persons were positive for KSHV. Unlike previous studies in North America and Europe, three (14%) of 22 non-KS cancer control patients' tissue specimens were also positive for KSHV that resulted in an overall odds ratio of 49.2 (95% confidence interval, 9.1 to 335) for detecting KSHV in KS lesions from patients in Uganda. <h3>Conclusion:</h3> As in North America and Europe, KSHV infection is strongly associated with both HIV-seropositive and HIV-seronegative KS in Africa. However, it is likely that infection with this virus is more highly prevalent in Uganda. (Arch Intern Med. 1996;156:202-204)
Blood coagulation profiling in patients using optical thromboelastography (OTEG) (Conference Presentation) (2016)

Impaired blood coagulation is often associated with increased postoperative mortality and morbidity in cardiovascular patients. The capability for blood coagulation profiling rapidly at the bedside will enable the timely detection of coagulation defects and open the opportunity for tailoring therapy to correct specific coagulation deficits Optical Thromboelastography (OTEG), is an optical approach to quantify blood coagulation status within minutes using a few drops of whole blood. The goal of the current study is to evaluate the diagnostic accuracy of OTEG for rapid coagulation profiling in patients. In OTEG, temporal laser speckle intensity fluctuations from a drop of clotting blood are measured using a CMOS camera. To quantify coagulation status, the speckle intensity autocorrelation function is measured, the mean square displacement of scattering particles is extracted, and viscoelastic modulus (G), during coagulation is measured via the generalized Stokes-Einstein relation. By quantifying time-resolved changes in G, the coagulation parameters, reaction time (R), clot progression time (K), clot progression rate (Angle), and maximum clot strength (MA) are derived. In this study, the above coagulation parameters were measured using OTEG in 269 patients and compared with standard mechanical Thromboelastography (TEG). Our results showed a strong correlation between OTEG and TEG measurements for all parameters: R-time (R=0.80, p<0.001), clotting time (R=0.78, p<0.001), Angle (R=0.58, p<0.001), and MA (R=0.60, p<0.001). These results demonstrate the unique capability of OTEG for rapid quantification of blood coagulation status to potentially improve clinical capability for identifying impaired coagulation in cardiovascular patients at the point of care.
Microbead-guided reconstruction of the 3D osteocyte network during microfluidic perfusion culture (2015)

Osteocytes reside as 3-dimensionally networked cells in the lacunocanalicular structure of bones, and function as the master regulators of homeostatic bone remodeling. We report here, for the first time to our best knowledge, the use of a biomimetic approach to reconstruct the 3D osteocyte network with physiological relevant microscale dimensions. In this approach, biphasic calcium phosphate microbeads were assembled with murine early osteocytes (MLO-A5) to provide an initial mechanical framework for 3D network formation and maintenance during long-term perfusion culture in a microfluidic chamber. The microbead size of 20-25 μm was used to: (1) facilitate a single cell to be placed within the interstitial space between the microbeads, (2) mitigate the proliferation of the entrapped cell due to its physical confinement in the interstitial site, and (3) control cell-to-cell distance to be 20-25 μm as observed in murine bones. The entrapped cells formed a 3D cellular network by extending and connecting their processes through openings between the microbeads within 3 days of culture. The entrapped cells produced significant mineralized extracellular matrix to fill up the interstitial spaces, resulting in the formation of a dense tissue structure during the course of 3-week culture. We found that the time-dependent osteocytic transitions of the cells exhibited trends consistent with in vivo observations, particularly with high expression of Sost gene, which is a key osteocyte-specific marker for the mechanotransduction function of osteocytes. In contrast, cells cultured in 2D well-plates did not replicate in vivo trends. These results provide an important new insight in building physiologically relevant in vitro bone tissue models.
Next-Generation Sequencing of<i>Coccidioides immitis</i>Isolated during Cluster Investigation (2011)

Next-generation sequencing enables use of whole-genome sequence typing (WGST) as a viable and discriminatory tool for genotyping and molecular epidemiologic analysis. We used WGST to confirm the linkage of a cluster of Coccidioides immitis isolates from 3 patients who received organ transplants from a single donor who later had positive test results for coccidioidomycosis. Isolates from the 3 patients were nearly genetically identical (a total of 3 single-nucleotide polymorphisms identified among them), thereby demonstrating direct descent of the 3 isolates from an original isolate. We used WGST to demonstrate the genotypic relatedness of C. immitis isolates that were also epidemiologically linked. Thus, WGST offers unique benefits to public health for investigation of clusters considered to be linked to a single source.
A hybrid, inverse approach to the design of magnetic resonance imaging magnets (2000)

This paper describes a hybrid numerical method of an inverse approach to the design of compact magnetic resonance imaging magnets. The problem is formulated as a field synthesis and the desired current density on the surface of a cylinder is first calculated by solving a Fredholm equation of the first kind. Nonlinear optimization methods are then invoked to fit practical magnet coils to the desired current density. The field calculations are performed using a semi-analytical method. The emphasis of this work is on the optimal design of short MRI magnets. Details of the hybrid numerical model are presented, and the model is used to investigate compact, symmetric MRI magnets as well as asymmetric magnets. The results highlight that the method can be used to obtain a compact MRI magnet structure and a very homogeneous magnetic field over the central imaging volume in clinical systems of approximately 1 m in length, significantly shorter than current designs. Viable asymmetric magnet designs, in which the edge of the homogeneous region is very close to one end of the magnet system are also presented. Unshielded designs are the focus of this work. This method is flexible and may be applied to magnets of other geometries.
A unique restriction endonuclease,<i>Bcg</i>l, from Bacillus<i>coagulans</i> (1993)

We have purified and characterized a new restriction endonuclease, BcgI, which has properties unlike those of the three recognized classes of restriction enzymes. BcgI was isolated from Bacillus coagulans, and it recognizes the sequence CGAN6TGC. BcgI cleaves double stranded DNA on both strands upstream and downstream of the recognition sequence, so that the recognition sequence is released as a 34-base pair fragment with 2-base 3'-extensions. Mg++ and S-adenosylmethionine are required for cleavage. Sinefungin, a structural analogue of AdoMet which generally inhibits methylase activity, can replace AdoMet in the cleavage reaction. The apparent binding constant (Kappd) for AdoMet is about 100 nM, while the KappD for sinefungin is about 500 nM.
Sensor fault diagnosis using Bayesian belief networks (1997)

This paper describes a method based on Bayesian belief networks (BBNs) sensor fault detection, isolation, classification, and accommodation (SFDIA). For this purpose, a BBN uses three basic types of nodes to represent the information associated with each sensor: (1) sensor-reading nodes that represent the mechanisms by which the information is communicated to the BBN, (2) sensor-status nodes that convey the status of the corresponding sensors at any given time, and (3) process-variable nodes that are a conceptual representation of the actual values of the process variables, which are unknown.
Domain position detection MAMMOS (2003)

This paper introduces a new technique for reading and writing data in a MAMMOS system in which the position rather than the presence of domains is detected. We will refer to this new technique as domain position detection or DPD-MAMMOS. DPD-MAMMOS has several advantages over conventional MAMMOS and mitigates a number of common problems. Through computer simulation, it is shown how this technique can increase power margins and increase storage density. At the same time, DPD-MAMMOS eliminates the need for clock recovery, and relaxes the requirements on coil design.
Heating of Low-Resistivity Semiconductor Ribbons and Wafers with Traveling Microwaves (1986)

A technique for using traveling microwaves to heat low-resistivity semiconductor ribbons (which are rectangular or nearly so) or wafers (which are round or nearly so) without a susceptor is described. The technique is believed to hold promise for uniformly heating as many as thirty samples simultaneously. The applicator is essentially a section of rectangular waveguide. Its relatively simple geometry facilitates the formulation of an appropriate boundary-value problem. Solution of this problem by numerical methods leads to values for the complex propagation constant as a function of various parameters of interest. Theory indicates that the absorption of microwave energy in the samples can be nearly uniform if the width of the waveguide is properly chosen. Measurements of attenuation constant, and voltage-standing-wave-ratio made at 2.45 Ghz are in satisfactory agreement with theoretical predictions. Preliminary measurements of temperature distributions using temperature sensitive lacquers are consistent with theoretical predictions.
Human interleukin 1. Purification to homogeneity. (1985)

We have purified human interleukin 1 (IL-1) to homogeneity by a simplified procedure that results in excellent yields of pure material that retains a high level of biological activity. IL-1, secreted by human peripheral blood macrophages that have been stimulated with Staphylococcus aureus, was purified by ion exchange chromatography and affinity chromatography on Procion Red agarose. The pure protein has a specific activity of 3.2 X 10(8) U/mg in the thymocyte mitogenesis assay, and is pyrogenic. No molecular weight heterogeneity was observed, in contrast to findings for mouse IL-1 and earlier reports of human IL-1. Purified IL-1, as analyzed by two-dimensional electrophoresis/electrofocusing gels, exhibited a series of charged species with isoelectric points ranging from 6.0 to 4.9, all with a molecular weight of approximately 17,500. Amino acid analysis indicated an abundance of acidic residues, in agreement with the low isoelectric points. There is little or no cysteine in the molecule. No evidence was found for the presence of carbohydrate moieties. The overall yield for this procedure was approximately 31% of the activity contained in the initial culture supernatant.
Verification of Multithreaded Object-Oriented Programs with Invariants (2004)

Developing safe multithreaded software systems is difficult due to the potential unwanted interference among concurrent threads. This paper presents a sound, modular, and simple verification tech-nique for multithreaded object-oriented programs with object in-variants. Based on a recent methodology for object invariants in single-threaded programs, this new verification technique enables leak-proof ownership domains. These domains guarantee that only one thread at a time can access a confined object. A primary aim of a reliable software system is ensuring that all objects in the system maintain consistent states: states in which all fields, and all fields of other objects on which they depend, contain legal meaningful values. In this paper, we formalize consistency
Interaction of urinary crystals with renal epithelial cells in the pathogenesis of nephrolithiasis. (1996)

Renal tubular fluid in the distal nephron is supersaturated with calcium and oxalate ions that nucleate to form crystals of calcium oxalate monohydrate (COM), the most common crystal in renal stones. It is not known how these nascent crystals are retained in the nephron to form calculi in certain individuals. Recent studies from this laboratory indicate that COM crystals can bind within seconds to anionic, sialic acid-containing glycoproteins on the apical surface of kidney epithelial cells in culture, suggesting one mechanisms whereby crystals could be retained in the tubule. Adherence of crystals to renal epithelial cells is inhibited by specific urinary anions such as glycosaminoglycans, uropontin, nephrocalcin, and citrate, each of which binds to the crystalline surface. Thus competition for the crystal surface between soluble anions in tubular fluid and anions on the apical cell surface could determine whether or not a crystal binds to the cell. Once bound, crystals are quickly internalized by renal cells in culture; reorganization of the cytoskeleton, alterations in gene expression, and initiation of proliferation can then ensue. Each of these cellular events appears to be regulated by a different set of extracellular factors. Identification of molecules in tubular fluid and on the cell surface that modulate crystal-cell interactions, as well as their mechanism of action, appears critical for understanding the pathogenesis of nephrolithiasis.
Test System for Measuring Mechanical and Recording Characteristics of Optical Disks (1987)

We have developed two test systems for measuring, respectively, the mechanical and optical (recording) characteristics of optical disks. The mechanical characteristics test system measures axial and radial runout, etc. It has optical displacement sensors with accuracy of 0.1 um in the axial direction and 0.01 um in the radial direction. The optical (recording) characteristics test system measures reflectivity, CNR, error rate, defects, etc. The system has a SNR of better than 70 dB.
Evaluation of Room-Temperature Chloroaluminate Molten Salts as Electrolytes for High Energy Density Batteries (1990)

This report reviews past battery studies using room-temperature chloroaluminate electrolytes, pointing out problems experienced. The report then summarizes attempts to circumvent these problems. A cell is described that uses a sodium anode, a copper (II) chloride cathode, and room-temperature chloroaluminate electrolyte buffered to the neutral composition. Cells give an open circuit voltage greater than 2.75 volts and discharge near 1 milliAmperes per centimeters squared at voltages greater than 2 volts for more than 20 hours. Cell failure is attributed to the formation of a nonconductive coating on the sodium electrode. Suggestions for future studies are presented. While the room- temperature chloroaluminates appear suitable for high-voltage, low-current batteries, their physical properties may limit their potential for high energy density batteries. Keywords: Battery, LiCl, Electrode, KCl, Molten salt, Electrodes, Sodium, Chloroaluminate, Cadmium, High energy density batteries, Ionic liquids.