gebhart/patrepeval huggingface dataset:
Defective neutrophil motility in patients with primary ciliary dyskinesia (1983)

Microtubules are important in the regulation of the motile functions of a variety of cells, including leukocytes, ciliated cells and spermatozoa. Polymorphonuclear leukocyte function was studied in ten patients with primary ciliary dyskinesia, an inherited disorder of microtubules in sperm tails and cilia. Neutrophil chemotaxis in Boyden chambers was slightly reduced, but only one patient showed a migration below normal values. In vivo mobilization of polymorphonuclear leukocytes into skin windows was also slightly decreased. In contrast, neutrophil polarization and orientation was normal. The bactericidal activity of neutrophils from patients with primary ciliary dyskinesia was normal, while the ingestion of bacteria was decreased. The abnormalities of neutrophil function in patients with primary ciliary dyskinesia are related to motility. It is suggested that the microtubule defect responsible for the abnormal pattern of ciliary beating is a general abnormality also responsible for the depression of polymorphonuclear leukocyte motility.
Interpolating Residual Zenith Tropospheric Delays for Improved Wide Area Differential GPS Positioning (2004)

Tropospheric delay is one of the major error sources in satellite-based positioning systems. The delay of radio signals caused by the troposphere can range from 2 m at the zenith to 20 m at lower elevation angles (e.g. below 10 degrees). In current Wide Area Differential GPS systems, the tropospheric delays are corrected locally by the users with empirical tropospheric models, instead of using corrections generated from the network. This implementation results in residual tropospheric delay due to tropospheric modeling error. This paper studies the use of the Ordinary Kriging (OK) method to interpolate the residual zenith tropospheric delay (ZTD) within a wide area GPS network in an attempt to improve the positioning accuracy within the coverage. The ZTD solutions from 129 International GPS Service (IGS) sites across Europe for over 3 months were collected for this analysis. The results demonstrate that with the interpolating procedure applied to residual ZTDs, the overall standard deviations of zenith tropospheric corrections are improved from 3-4 cm, achievable with both the standard Saastamoinen and GTN model, down to 1-2 cm, while the overall bias of the Saastamoinen model is also dramatically reduced from 14 mm to nearly zero. This concludes that interpolating residual zenith tropospheric delays is an efficient way to improve Wide Area Differential GPS positioning.
A Sand Erosion Model for Volumetric Sand Predictions in a North Sea Reservoir (1999)

Abstract Volumetric sand production data from a North Sea reservoir are interpreted with respect to the applied drawdown. Two sand rates are identified, one related to the increase of the drawdown and one to the magnitude of the drawdown. A sand erosion model is presented and used for predicting the field data. The model results compare satisfactorily with the field observations.
Cellulase Enzyme from <i>Aspergillus niger</i> (1982)

Cellulase enzyme was produced by a selected strain of Aspergillus niger isolated from deteriorated wood and grown on different carbon sources. Filter paper gave the highest yield, followed by carboxymethyl cellulose (CMC). Cellobiose as well as glucose gave a low yield, while the yield from lactose was negligible. The concentration of filter paper cellulose that induced the maximum yield of the enzyme was 1%. Both soluble cellulose (CMC) and cotton cellulose treated with phosphoric acid (swollen) were easily hydrolyzed by cellulase; an increase in cellulase concentration lead to more hydrolysis of CMC and gave linearity in the reaction velocity. At certain concentrations of the enzyme, increase in CMC concentration, (up to 1%) resulted in more reducing sugar. Beyond this point no more hydrolysis occur.
Photodynamic therapy with 5‐aminolevulinic acid and diamino acid derivatives of protoporphyrin IX reduces papillomas in mice without eliminating transformation into squamous cell carcinoma of the skin (2009)

Photodynamic therapy (PDT) is used to treat malignant and nonmalignant diseases. It is also used for cosmetological skin treatment. PDT is generally considered to have a low risk of carcinogenicity. However, instances of nonmalignant human tumors turning malignant have been linked to PDT. In this study, we used 5-aminolevulinic (ALA) acid and 3 water soluble photosensitizers-PP(Arg)(2), PP(Ser)(2)Arg(2), PP(Ala)(2)Arg(2), all diamino acid derivatives of protoporphyrin IX-to treat benign papillomas in FVB/N mice induced by 7,12-dimethylbenz(a)anthracene (DMBA)-12-O-tetradecanoyl-phorbol-13-acetate (TPA). Of these drugs, ALA and PP(Arg)(2) were found the most efficient. PDT reduced the number of papillomas, but with increasing effectiveness of the drugs, the risk of malignant transformation of the papillomas into squamous cell carcinomas increased. The underlying mechanisms are not clear and further investigations are needed.
Sequence scanning: A method for rapid sequence acquisition from large-fragment DNA clones. (1996)

A strategy of "sequence scanning" is proposed for rapid acquisition of sequence from clones such as bacteriophage P1 clones, cosmids, or yeast artificial chromosomes. The approach makes use of a special vector, called LambdaScan, that reliably yields subclones with inserts in the size range 8-12 kb. A number of subclones, typically 96 or 192, are chosen at random, and the ends of the inserts are sequenced using vector-specific primers. Then long-range spectrum PCR is used to order and orient the clones. This combination of shotgun and directed sequencing results in a high-resolution physical map suitable for the identification of coding regions or for comparison of sequence organization among genomes. Computer simulations indicate that, for a target clone of 100 kb, the scanning of 192 subclones with sequencing reads as short as 350 bp results in an approximate ratio of 1:2:1 of regions of double-stranded sequence, single-stranded sequence, and gaps. Longer sequencing reads tip the ratio strongly toward increased double-stranded sequence.
A Consideration of VCO and Thermal Phase Noise in a Coherent Two-Way Doppler Communication System (1965)

An analysis of a coherent two-way (transponder) Doppler communication system composed of a ground transmitter, a spacecraft transponder, and a ground receiver has been made to determine the effects of VCO phase and thermal phase noise at the ground receiver output (See Fig. 2). This system is typical of those used on lunar and planetary space programs. The analysis shows that the phase noise contribution of the ground receiver's VCO is inversely proportional to the ground receiver's noise bandwidth [See (15)]. Further it has been shown that the spacecraft VCO phase noise, spacecraft thermal phase noise, and ground receiver thermal phase noise are all functions of the ratio of transponder-to-ground-receiver noise bandwidths [See (13), (4) and (5)]. All the relationships were derived using complex integration techniques.
Reconstitution of an Infectious Human Endogenous Retrovirus (2007)

The human genome represents a fossil record of ancient retroviruses that once replicated in the ancestors of contemporary humans. Indeed, approximately 8% of human DNA is composed of sequences that are recognizably retroviral. Despite occasional reports associating human endogenous retrovirus (HERV) expression with human disease, almost all HERV genomes contain obviously inactivating mutations, and none are thought to be capable of replication. Nonetheless, one family of HERVs, namely HERV-K(HML-2), may have replicated in human ancestors less than 1 million years ago. By deriving a consensus sequence, we reconstructed a proviral clone (HERV-KCON) that likely resembles the progenitor of HERV-K(HML-2) variants that entered the human genome within the last few million years. We show that HERV-KCON Gag and protease proteins mediate efficient assembly and processing into retrovirus-like particles. Moreover, reporter genes inserted into the HERV-KCON genome and packaged into HERV-K particles are capable of infectious transfer and stable integration in a manner that requires reverse transcription. Additionally, we show that HERV-KCON Env is capable of pseudotyping HIV-1 particles and mediating entry into human and nonhuman cell lines. Furthermore, we show that HERV-KCON is resistant to inhibition by the human retrovirus restriction factors tripartite motif 5alpha and apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) 3G but is inhibited by APOBEC 3F. Overall, the resurrection of this extinct infectious agent in a functional form from molecular fossils should enable studies of the molecular virology and pathogenic potential of this ancient human retrovirus.
2-Nested Simulation is not Finitely Equationally Axiomatizable (2000)

<p>2-nested simulation was introduced by Groote and Vaandrager<br /> [10] as the coarsest equivalence included in completed trace equivalence<br /> for which the tyft/tyxt format is a congruence format. In the linear<br />time-branching time spectrum of van Glabbeek [8], 2-nested simulation<br />is one of the few equivalences for which no finite equational axiomatization<br /> is presented. In this paper we prove that such an axiomatization<br />does not exist for 2-nested simulation.</p><p>Keywords: Concurrency, process algebra, basic CCS, 2-nested simulation,<br /> equational logic, complete axiomatizations.</p>
Measurement of corneal thickness by low-coherence interferometry (1992)

A special interferometric technique, which uses light of low-coherence length and the Doppler principle, is applied to measurement of the thickness of the human cornea in vivo. The special construction of the instrument eliminates any influence from eye motions on the thickness results. With a superluminescent diode as a light source, a precision of ~ 1.5 microm is obtained. This is ~ 3-8 times better than the precision of existing instruments. Since interobserver and interinstrument variability are avoided by the measurement principle, the improvement in total accuracy, compared with that when existing instruments are used, should be even better.
The next 22 years (1978)

Attempt s to predict the future must have started as soon as men found themselves capable of speech. Unfortunately, the evidence suggests that this is one human activity which has not improved with practice. But the temptation to go on trying is very great because there is obviously so much to be gained by anticipating the future. The fact is that the ability to think ahead has always been an important factor in success or even survival.
A calcium-dependent protease as a potential therapeutic target for Wolfram syndrome (2014)

Wolfram syndrome is a genetic disorder characterized by diabetes and neurodegeneration and considered as an endoplasmic reticulum (ER) disease. Despite the underlying importance of ER dysfunction in Wolfram syndrome and the identification of two causative genes, Wolfram syndrome 1 (WFS1) and Wolfram syndrome 2 (WFS2), a molecular mechanism linking the ER to death of neurons and β cells has not been elucidated. Here we implicate calpain 2 in the mechanism of cell death in Wolfram syndrome. Calpain 2 is negatively regulated by WFS2, and elevated activation of calpain 2 by WFS2-knockdown correlates with cell death. Calpain activation is also induced by high cytosolic calcium mediated by the loss of function of WFS1. Calpain hyperactivation is observed in the WFS1 knockout mouse as well as in neural progenitor cells derived from induced pluripotent stem (iPS) cells of Wolfram syndrome patients. A small-scale small-molecule screen targeting ER calcium homeostasis reveals that dantrolene can prevent cell death in neural progenitor cells derived from Wolfram syndrome iPS cells. Our results demonstrate that calpain and the pathway leading its activation provides potential therapeutic targets for Wolfram syndrome and other ER diseases.
Counting molecules in cell-free DNA and single cells RNA (2016)

<p>The field of Molecular Biology got started in earnest with the discovery of the molecular structure of DNA. This lead to a surge of interest into the relationships between DNA, RNA and proteins, and to the development of fundamental tools for manipulating those substances, such as cutting, ligating, amplifying, visualizing and size-selecting DNA. With these tools at hand it was possible to begin sequencing DNA, a process that took a leap forward in 2005 with the advent of Next Generation Sequencing (NGS). An inherent problem with NGS is that both the sequencing process and the library preparation introduce errors and biases. The massive amount of data generated by NGS, and the use of NGS in clinical settings, has created a demand for methods that can account for this and thereby making the sequencing data correct and reproducible.</p><p>Part 1 of this thesis briefly describes the development of Molecular Biology from the discovery of the molecular structure of DNA until today. Part 2 describes the development of error correcting and molecule counting methods, and part 3 describes the results of the papers of the thesis.</p><p>Paper I introduces the concept of Unique Molecular Identifiers (UMI) for reducing noise in molecular karyotyping and RNA sequencing data. Paper II compares the use of UMIs, a novel amplification-free method, and standard library preparation in Non-Invasive Prenatal Testing (NIPT) of fetal karyotype. Paper III uses the UMI concept together with single-cell tagged reverse transcription (STRT) to examine promoter preference in single cells. Finally paper IV use UMIs combined with PacBio sequencing to examine the full-length transcriptome in single cells.</p><h3>List of scientific papers</h3><p>I. Kivioja, T., Vaharautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S., and Taipale, J. (2012). Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 9, 72-74. <br><a href="https://doi.org/10.1038/nmeth.1778">https://doi.org/10.1038/nmeth.1778</a><br><br> </p><p>II. Karlsson, K., Sahlin, E., Iwarsson, E., Westgren, M., Nordenskjöld, M., and Linnarsson, S. (2015). Amplification-free sequencing of cell-free DNA for prenatal noninvasive diagnosis of chromosomal aberrations. Genomics 105, 150-158. <br><a href="https://doi.org/10.1016/j.ygeno.2014.12.005">https://doi.org/10.1016/j.ygeno.2014.12.005</a><br><br> </p><p>III. Kasper Karlsson, Peter Lönnerberg, Sten Linnarsson. Alternative Promoters are co-regulated in single cells. [Manuscript]</p><p>IV. Kasper Karlsson, Sten Linnarsson. Single-cell mRNA isoform diversity in the mouse brain. [Manuscript]</p>
Nerve Growth Factor Stimulates the Tyrosine Phosphorylation of Endogenous Crk-II and Augments Its Association with p130Cas in PC-12 Cells (1996)

The cellular homologs of the v-Crk oncogene product consist primarily of Src homology region 2 (SH2) and 3 (SH3) domains. v-Crk overexpression causes cell transformation and elevation of tyrosine phosphorylation in fibroblasts and accelerates differentiation of PC-12 cells in response to nerve growth factor (NGF). To further explore the role of Crk in NGF-induced PC-12 cell differentiation, we found that both NGF and epidermal growth factor stimulate the tyrosine phosphorylation of endogenous Crk II. Moreover, hormone stimulation enhanced the specific association of Crk proteins with the tyrosine-phosphorylated p130Cas, the major phosphotyrosine-containing protein in cells transformed with v-Crk. This interaction is mediated by the SH2 domain of Crk and can be inhibited with a phosphopeptide containing the Crk-SH2 binding motif. Furthermore, the Crk-SH2 domain binds tyrosine-phosphorylated paxillin, a cytoskeletal protein, following treatment of PC-12 cells with NGF or epidermal growth factor. These data suggest that Crk functions in a number of signaling processes in PC-12 cells.
Polyurethane Macroinitiator for Controlled Monomer Insertion of Styrene (2003)

Polyurethane containing alkoxyamine units in the main chain were prepared by polyaddition of diisocyanate with TEMPO-based diol. Radical polymerization of styrene was carried out in bulk with TEMPO-based polyurethane as macroinitiator. GPC, NMR, and IR data revealed that the insertion reaction was accurately controlled to afford the segmented copolymers composed of both urethane groups and polystyrene segments. From the results of model polymerization, it is inferred that the well-defined polystyrene chains were inserted into the macroinitiator. The obtained polymers showed quite different solubility in solvents compared with the macroinitiator and styrene homopolymer. The solubility in polar solvents decreases gradually with increasing inserted polystyrene chain length.
ABS Naval Vessel Rules (NVR) for Mission Critical Networks, Software Development, and Safety Critical Control Systems (2007)

The following paper provides a rationale, background, and summary of how modern information technology is being used effectively by the U.S. navy in mission critical applications for shipboard control, navigation, and interior communication systems. The paper provides a background and summary of the updated American Bureau of Shipping (ABS) naval vessel rules (NVR) requirements for mission critical networks, software development, and safety critical control systems. The Naval Sea Systems Command (NAVSEA) and the American Bureau of Shipping (ABS) have partnered to co-write these rules which were initially drafted by comparing the existing commercial steel vessel rules (SVR) in these areas with current United States Navy shipbuilding practice from recent shipbuilding programs. The requirements for safety critical systems were then derived from the safety of flight (SoF) criteria for U.S. Navy submarine ship control systems. The paper explains the relationship between the Naval Technical Authority and the American Bureau of Shipping and their respective roles in the certification of control, automation, and navigation systems software and networks. The current requirements prescribed in the naval vessel rules are compared and contrasted with the commercial steel vessel rules and the merits and rationale behind each approach are discussed.
Studies on polyyne polymers containing transition metals in the main chain. VII. Synthesis and characterization of palladium‐polyyne polymers (1982)

Abstract Metal‐polyyne polymers consisting of palladium and conjugated acetylenic systems, magnified image where P D and R represent the —Pd(PBu 3 ) 2 —moiety and alkyl groups, respectively, were prepared by polycondensation between palladium chlorides and α,ω‐diethynyl compounds in amines using a catalytic amount of cuprous iodide. The molecular weights of the polymers formed were greatly affected by the basicity of the amines and the addition of free phosphines to the polymerization system. Under the optimum conditions, i.e., in the presence of CuI and PBu 3 (in molar ratio 1/4) in piperidine at room temperature, polymer Ia (R 1 = R 2 = H) having M̄ w = 29,000 was obtained.
Targeted disruption of the mouse sphingolipid activator protein gene: a complex phenotype, including severe leukodystrophy and wide-spread storage of multiple sphingolipids (1996)

The four established or putative sphingolipid activator proteins derive from a large precursor protein encoded by a single gene. In addition to generating the four sphingolipid activator proteins, the precursor protein is suspected of having functions of its own, as, for example, a lipid binding/transport protein or a neurotrophic factor. The gene also appears to encode the Sertoli cell major sulfated glycoprotein. Sequence similarities have been noted with many other proteins of diverse functions. One patient and a fetus in a single family with a complete defect of this gene due to a mutation in the initiation codon exhibited complex pathological and biochemical abnormalities. Mutant mice homozygous for an inactivated gene of the sphingolipid activator protein precursor exhibit two distinct clinical phenotypes-neonatally fatal and later-onset. The latter develop rapidly progressive neurological signs around 20 days and die by 35-38 days. At 30 days, severe hypomyelination and periodic acid-Schiff-positive materials throughout the nervous system and in abnormal cells in the liver and spleen are the main pathology. Most prominently lactosylceramide, and additionally ceramide, glucosylceramide, galactosylceramide, sulfatide, and globotriaosylceramide are abnormally increased in the brain, liver, kidney, and their catabolism abnormally slow in cultured fibroblasts. Brain gangliosides are generally increased, particularly the monosialogangliosides. The clinical, pathological and biochemical phenotype closely resembles that of the human disease. This model not only allows further clarification of the physiological functions of the four individual sphingolipid activator proteins but also should be useful to explore putative functions of the precursor protein.
Activity of HMR 3647 Compared to Those of Five Agents against <i>Haemophilus influenzae</i> and <i>Moraxella catarrhalis</i> by MIC Determination and Time-Kill Assay (1998)

The microdilution MICs of HMR 3647, erythromycin A, azithromycin, clarithromycin, roxithromycin, and pristinamycin against 50/90% of 249 Haemophilus influenzae and 50 Moraxella catarrhalis isolates were 2/4, 0.06/0.125; 8/16, 0.25/0.25; 2/4, 0.06/0.125; 16/16, 0.25/0.25; 32/>32, 1/2; and 2/4, 0.5/0.5 microg/ml. Azithromycin was bactericidal against all 10 H. influenzae and 3 of 5 M. catarrhalis isolates and HMR 3647, erythromycin A, clarithromycin, roxithromycin, and pristinamycin were bacteriostatic, against all 15 strains after 24 h at the MIC.
Mesoporous NiCo<sub>2</sub>O<sub>4</sub> Nanowire Arrays Grown on Carbon Textiles as Binder‐Free Flexible Electrodes for Energy Storage (2013)

Binary metal oxides has been regarded as a promising class of electrode materials for high‐performance energy storage devices since it offers higher electrochemical activity and higher capacity than mono‐metal oxide. Besides, rational design of electrode architectures is an effective solution to further enhance electrochemical performance of energy storage devices. Here, the advanced electrode architectures consisting of carbon textiles uniformally covered by mesoporous NiCo 2 O 4 nanowire arrays (NWAs) are successfully fabricated by a simple surfactant‐assisted hydrothermal method combined with a short post annealing treatment, which can be directly applied as self‐supported electrodes for energy storage devices, such as Li‐ion batteries, supercapacitors. The as‐prepared mesoporous NiCo 2 O 4 nanowires consist of numerous highly crystalline nanoparticles, leaving a large number of mesopores to alleviate the volume change during the charge/discharge process. Electrode architectures presented here promise fast electron transport by direct connection to the growth substrate and facile ion diffusion path provided by both the abundant mesoporous structure in nanowires and large open spaces between neighboring nanowires, which ensures every nanowire participates in the ultrafast electrochemical reaction. Benefiting from the intrinsic materials and architectures features, the unique binder‐free NiCo 2 O 4 /carbon textiles exhibit high specific capacity/capacitance, excellent rate capability, and cycling stability.