gebhart/patrepeval huggingface dataset:
Invasive <i>Shigella flexneri</i> Activates NF-κB Through a Lipopolysaccharide-Dependent Innate Intracellular Response and Leads to IL-8 Expression in Epithelial Cells (2000)

The pathogenesis of Shigella flexneri infection centers on the ability of this organism to invade epithelial cells and initiate an intense inflammatory reaction. Because NF-kappa B is an important transcriptional regulator of genes involved in inflammation, we investigated the role of this transcription factor during S. flexneri infection of epithelial cells. Infection of HeLa cells with invasive S. flexneri induced NF-kappa B DNA-binding activity; noninvasive S. flexneri strains did not lead to this activation. The pathway leading to NF-kappa B activation by invasive S. flexneri involved the kinases, NF-kappa B-inducing kinase, I kappa B kinase-1, and I kappa B kinase-2. NF-kappa B activation was linked to inflammation, because invasive S. flexneri activated an IL-8 promoter-driven reporter gene, and the kappa B site within this promoter was indispensable for its induction. Microinjection of bacterial culture supernatants into HeLa cells suggested that LPS is responsible for NF-kappa B activation by S. flexneri infection. In conclusion, the eukaryotic transcription factor NF-kappa B was activated during S. flexneri infection of epithelial cells, which suggests a role for this transcriptional regulator in modulating the immune response during infection in vivo.
Secondary structure assignment for .alpha./.beta. proteins by a combinatorial approach (1983)

We describe an algorithm for assigning the secondary structure of alpha/beta proteins. Turns are identified very accurately (98%) by simultaneously considering hydrophilicity and the ideal spacing of turns throughout the sequence. The segments bounded by these turns are labeled by a pattern-recognition scheme based on the physical properties of alpha-helices and beta-strands, in this class of proteins. Long-range, as well as local, information is incorporated to enhance the quality of the assignments. Although the assignment for any one sequence is not unique, at least one of the assignments bears a close resemblance to the native structure. The algorithm successfully divides protein sequences into two classes: alpha/beta and non-alpha/beta. The accuracy of the secondary-structure assignments in the alpha/beta class is sufficient to provide useful input for tertiary-structure assignments.
Genomics: the science and technology behind the human genome project (1999)

DNA Chemistry and Biology. A Genome Overview at the Level of Chromosomes. Analysis of DNA Sequences by Hybridization. Polymerase Chain Reaction and Other Methods for In Vitro DNA Amplification. Principles of DNA Electrophoresis. Genetic Analysis. Cytogenetics and Pseudogenetics. Physical Mapping. Enhanced Methods for Physical Mapping. DNA Sequencing: Current Tactics. Strategies for Large--Scale DNA Sequencing. Future DNA Sequencing Without Length Fractionation. Finding Genes and Mutations. Sequence--Specific Manipulation of DNA. Results and Implications of Large--Scale DNA Sequencing. Appendix. Index.
Effect of tofacitinib, a Janus kinase inhibitor, on haematological parameters during 12 weeks of psoriasis treatment (2013)

Tofacitinib conferred tolerable, dose-dependent changes in haematological parameters during short-term administration in patients with psoriasis. The effects did not appear to be progressive, and were often transient or reversible.
Using artificial neural networks to improve hardware branch predictors (2003)

Among the current techniques to predict the outcome of branches in modern microprocessors, two-level branch predictors have shown to be one of the best mechanisms. The correct prediction of branches is a fundamental factor for achieving high performance. Branch interference is a major contributor to the number of branches mispredicted by two-level predictors. Increasing the size of the pattern history table (PHT) reduces the interference, but the number of transistors that can be assigned to the PHT and the frequency at which it can be accessed limits the increase on its size. Another method for reducing interference is that of the gshare predictor. The gshare predictor combines the information used to generate the index into the PHT to increase its efficiency. In this paper, neural networks are used to discover a prediction algorithm to reduce interference and therefore increase the performance of two-level branch predictors. The neural net learns about the dynamics of programs to be executed in a microprocessor. A table of comparative performance with other established prediction methods is provided.
Enterovirus RNA in serum is a risk factor for beta-cell autoimmunity and clinical type 1 diabetes: a prospective study. Childhood Diabetes in Finland (DiMe) Study Group. (2000)

Recent prospective studies have documented serologically an increased frequency of enterovirus infections in prediabetic children, indicating that these infections may initiate and accelerate the beta-cell damaging process several years before the clinical manifestation of type 1 diabetes. The aim of the present study was to establish whether these serological findings would be supported by the detection of enterovirus RNA in a unique prospective series of sera collected from prediabetic children 0-10 years before the manifestation of clinical type 1 diabetes. Reverse transcription followed by polymerase chain reaction employing highly conserved primers among enteroviruses were used to amplify enteroviral sequences. Viral RNA was found in 22% (11/49) of follow-up samples from prediabetic children but in only 2% (2/105) of those from controls (OR 14.9, P < 0.001). Persisting RNA positivity was not observed in any of these children. The presence of enterovirus RNA was associated with concomitant increases in the levels of autoantibodies against islet cells (OR 21.7, P < 0.01) and glutamic acid decarboxylase (OR 15.4, P < 0.05), but not in the levels of antibodies against insulin or the tyrosine phosphatase-like IA-2 protein. In contrast to the prediabetic children, those with newly diagnosed type 1 diabetes were negative for enterovirus RNA. The results thus complement previous serological data, suggesting that enterovirus infections are an important risk factor underlying type 1 diabetes and associated with the induction of beta-cell autoimmunity even years before symptoms appear.
Solvent effects on the thermodynamics of double-helix formation in (dG-dC)3 (1981)

The thermodynamics of double-helix formation by (dG-dC)3 have been measured in aqueous solvent mixtures containing 10 mol % methanol, ethanol, 1-propanol, formamide, N,N-dimethylformamide, or urea and 20 mol % ethanol. Optical activity measurements indicate the conformation of the double helix at 3 degree C is the same in all the solvent mixtures except 20 mol % ethanol. All the cosolvents destabilize the helix relative to water. With 10 mol % alcohol cosolvents, this destabilization is associated with a more unfavorable entropy change averaging approximately 8% and a more favorable enthalpy change averaging approximately 5%. This is consistent with a small contribution of hydrophobic bonding to stability. In contrast, the destabilization by formamide, N,N-dimethylformamide, and urea is associated with a more unfavorable enthalpy change averaging approximately 23% and a more favorable entropy change averaging approximately 21%. Since all three of these cosolvents have dipole moments larger than water, this is consistent with increased competition for dipolar interactions between the nucleic acid bases. None of the results correlate with any one bulk solvent parameter such as surface tension, viscosity, or dielectric constant. With 20 mol % ethanol, optical activity measurements are consistent with a partial B to C form transition. This is associated with a 27% less favorable enthalpy and 25% more favorable entropy for helix formation relative to water. Since the B to C transition is associated with helix dehydration, this may imply a significant contribution of bound water to stability.
Molecular species of the enzymatically synthesized polyunsaturated fatty acid rich triglyceride. (1991)

Enzymatic glyceride synthesis and acid interchange using icosapentaenoic acid (EPA), docosahexaenoic acid (DHA), -linolenic acid
Effect of Small-Molecule–Binding Affinity on Tumor Uptake <i>In Vivo</i> : A Systematic Study Using a Pretargeted Bispecific Antibody (2012)

Small-molecule ligands specific for tumor-associated surface receptors have wide applications in cancer diagnosis and therapy. Achieving high-affinity binding to the desired target is important for improving detection limits and for increasing therapeutic efficacy. However, the affinity required for maximal binding and retention remains unknown. Here, we present a systematic study of the effect of small-molecule affinity on tumor uptake in vivo with affinities spanning a range of three orders of magnitude. A pretargeted bispecific antibody with different binding affinities to different DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid)-based small molecules is used as a receptor proxy. In this particular system targeting carcinoembryonic antigen, a small-molecule-binding affinity of 400 pmol/L was sufficient to achieve maximal tumor targeting, and an improvement in affinity to 10 pmol/L showed no significant improvement in tumor uptake at 24 hours postinjection. We derive a simple mathematical model of tumor targeting using measurable parameters that correlates well with experimental observations. We use relations derived from the model to develop design criteria for the future development of small-molecule agents for targeted cancer therapeutics.
V-band single chip, direct carrier BPSK modulation transmitter with integrated patch antenna (2002)

A single chip V-Band pHEMT technology transmitter with wideband direct BPSK modulation and on-chip dual band patch antenna is reported. The transmitter features, 10% bandwidth electronic tuning range, substantial power output, injection locking capability, low power consumption and good patch antenna radiation characteristics. As such it is well suited to wireless digital communications systems as well in radar and phased array applications.
Structure of HLA antigens: amino-acid and carbohydrate compositions and NH2-terminal sequences of four antigen preparations. (1976)

Amino-acid and carbohydrate compositions in addition to limited NH2-terminal sequence data of four preparations of HLA antigens, including products of both of the major histocompatibility loci (HLA-A and HLA-B), show that the antigens have great homology in the primary structure. A striking observation is that HLA antigens also have a considerable structure homology with mouse H-2 antigens. HLA antigens appear to have one carbohydrate side chain which has the same composition in all four cases. The possible relation of the structure of the heavy chain of HLA antigens to immunoglobulins is discussed, based on the limited data which are available so far.
Spontaneous Formation of Quasi-Bookshelf Layer Structure in New Ferroelectric Liquid Crystals Derived from a Naphthalene Ring (1990)

A quasi-bookshelf layer structure has been obtained by a conventional rubbing method at room temperature in a FLC mixture composed of naphthalene-derived liquid crystals. This layer structure is spontaneously formed due to a unique temperature dependence of the interlayer spacing; X-ray diffraction indicates that the layer spacing decreases from 34 to 33.5 Å and then increases to 33.8 Å with decreasing temperature in SmC * . Contrary to the unusual behavior of the layer spacing, the director tilt angle determined optically shows ordinary temperature dependence and attains a relatively large value, 17°, at room temperature.
Glial and neuroaxonal biomarkers in a multiple sclerosis (MS) cohort. (2020)

87 MS patients (aged 41.1±11.96) enrolled in the study and 21 controls (aged 44.17±12.8). The female/male ratio was 8 females/12 males in the controls and 64 females/20 males in the patients' group. From the patients' cohort 86% (75 patients) were relapsing forms and 14% (12 patients) were progressive forms of the disease. From the total sample 60 patients had disease duration more than a year and 48 less or equal to 1 year. 31 (28.9%) patients had received prior corticosteroid course and 15 patients (13.9%) had prior statin use. In the MS cohort 31 patients (28.7%) had received previous first line disease modifying treatment. The EDSS that showed mild disability without effect of mobility on grades below 4, affected the majority of the sample with EDSS 1-3 in 70% of the patients. 27% of the patients had EDSS scale score 3.5-6.
Paired Immunoglobulin-like Receptor (PIR)-A Is Involved in Activating Mast Cells through Its Association with Fc Receptor γ Chain (1998)

Paired immunoglobulin-like receptor (PIR)-A and PIR-B possess similar ectodomains with six immunoglobulin-like loops, but have distinct transmembrane and cytoplasmic domains. PIR-B bears immunoreceptor tyrosine-based inhibitory motif (ITIM) sequences in its cytoplasmic domain that recruit Src homology (SH)2 domain-containing tyrosine phosphatases SHP-1 and SHP-2, leading to inhibition of B and mast cell activation. In contrast, the PIR-A protein has a charged Arg residue in its transmembrane region and a short cytoplasmic domain that lacks ITIM sequences. Here we show that Fc receptor gamma chain, containing an immunoreceptor tyrosine-based activation motif (ITAM), associates with PIR-A. Cross-linking of this PIR-A complex results in mast cell activation such as calcium mobilization in an ITAM-dependent manner. Thus, our data provide evidence for the existence of two opposite signaling pathways upon PIR aggregation. PIR-A induces the stimulatory signal by using ITAM in the associated gamma chain, whereas PIR-B mediates the inhibitory signal through its ITIMs.
De l'execució de penes a la reinserció (2013)

Aquest llibre recull les ponencies i els debats que van constituir el seminari «De l’execucio de penes a la reinsercio», que va tenir lloc al Centre d’Estudis Juridics i Formacio Especialitzada (CEJFE) els dies 6 i 7 de juny de 2013. La iniciativa d’organitzar aquest seminari va sorgir del Grup Interuniversitari de Recerca en Criminologia Aplicada a la Penologia i del CEJFE amb la pretensio d’unir en un mateix espai de debat tres grups de professionals que actuen i reflexionen en relacio amb l’execucio de penes a Catalunya, pero que habitualment mantenen poc contacte entre ells: l’Administracio competent en aquest tema; la judicatura i la fiscalia; i l’ambit de la recerca. Els objectius del seminari eren tres: fomentar el dialeg entre aquests tres grups de professionals; que existis transferencia —d’iniciatives, de preocupacions i de coneixement— entre un ambit mes orientat a la reflexio (l’ambit de recerca) i dos ambits mes orientats a la practica (l’Administracio d’una banda, i la fiscalia i la judicatura, de l’altra); i s’aspirava al fet que de la reflexio conjunta sorgissin noves propostes per millorar la capacitat del nostre sistema d’execucio de penes per assolir la reinsercio social de les persones penades. Per assolir-los es va estructurar al voltant de tres temes, considerats com a reptes principals del nostre sistema d’execucio penal en clau de promoure la reinsercio: El cami cap a la llibertat condicional; Ampliacio de l’us de les mesures penals alternatives a la preso i supervisio efectiva a la comunitat; i Marc legal i gestio dels delinquents d’alt risc: present i futur. Amb la publicacio d’aquest llibre es preten que les idees i les discussions tingudes en el seminari puguin arribar a l’ampli col·lectiu de persones que, des de la recerca o des de la practica, focalitzen la seva tasca professional en l’execucio penal i en el sistema de reinsercio, pensant que alguna de les aportacions pugui ser d’utilitat en el desenvolupament de la seva feina.
A voltage reduction technique for digital systems (1990)

A self-regulating on-chip voltage-reduction circuit that adjusts the internal supply voltage to the lowest value compatible with chip speed requirements is described. Besides enhancing reliability, this technique allows power savings. The technique is based on regulation of the supply voltage of an equivalent critical path, a small circuit with delay V/sub dd/ properties proportional to those of the actual critical path. The output of this equivalent critical path is compared with the output of a second identical equivalent critical path which is connected to the full supply voltage and serves as a reference. In a first-order approximation the ratio of the delay of a critical path to the period of a ring oscillator is a constant that depends only on the number of gates, the dimensions of the transistors, and the load capacitances. This means that a ring oscillator can be used as an equivalent critical path for all digital circuits. Moreover, when the supply voltage of a ring oscillator (VCO) is changed the frequency changes. The voltage regulator principle can be implemented with a phase-locked loop (PLL). By adjusting the VCO supply voltage, the PLL causes the VCO to oscillate at N*f/sub in/. If the dimensions of the VCO transistors and the division ratio N are such that the critical path functions correctly at the regulated voltage, it will always function correctly, as changing parameters temperature or frequency f/sub in/ affect the VCO in the same way as the circuitry.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Genetically stable and fully effective smallpox vaccine strain constructed from highly attenuated vaccinia LC16m8 (2005)

A highly attenuated LC16m8 (m8) smallpox vaccine has been licensed in Japan because of its extremely low neurovirulence profile, which is comparable to that of replication incompetent strains of vaccinia virus. From 1973 to 1975, m8 was administrated to >100,000 infants where it induced levels of immunity similar to that of the originating Lister strain, without any serious side effects. Recently, we observed that m8 reverts spontaneously to large plaque forming clones that possess virulence equivalent to that of LC16mO, a parental virus strain of m8. Here, we report that the B5R gene is responsible for the reversion, and that we could construct a more genetically stable virus by deleting B5R from m8. The protective immunogenicity of the vaccine candidate proved to be equivalent to that of the U.S.-licensed product Dryvax, and much superior to modified vaccinia Ankara in a mouse model. Furthermore, the vaccine strain never elicited any symptoms in severe combined immunodeficiency disease mice, even at a dose 1,000-fold greater than that used in the immune protection experiments, which is in contrast to the lethal pathogenicity induced by Dryvax inoculation of severe combined immunodeficiency disease mice. Our results suggest that this vaccine strain is a good candidate as a suitable smallpox vaccine and a vector virus, and that B5R is not essential for protective immunity against smallpox.
Interphase cytogenetics: a new tool for the study of genetic changes in brain tumors (1992)

Interphase cytogenetics is the application of nonradioactive in situ hybridization with chromosome-specific DNA probes to interphase nuclei. In this study, interphase cytogenetics was used to investigate 66 primary brain tumors (33 gliomas, 30 meningiomas, and three medulloblastomas) for numerical chromosomal aberrations of chromosomes 1, 6, 7, 10, 11, 17, 18, X, and Y. Of the 33 gliomas (17 astrocytomas grades II, III, and IV, five oligoastrocytomas, seven oligodendrogliomas, and four ependymal tumors), 22 were near diploid, while the remaining 11 showed a significant triploid or tetraploid component. The predominant specific aberrations in gliomas were an over-representation of chromosome 7 (13 cases) and an under-representation of chromosome 10 (16 cases). These changes were observed in grade III and grade IV astrocytomas, as well as in oligodendrogliomas. Other frequent numerical changes were a gain of chromosome 17 (six cases) and a loss of chromosome 18 (seven cases). This loss of chromosome 18 seemed relatively specific for gliomas with an oligodendroglial component (six cases). Only two of 33 gliomas displayed no genetic abnormality with the probes used. Seven patients with astrocytomas died of their brain tumor during the clinical follow-up period. Their astrocytomas did not show a different chromosomal constitution compared to the other gliomas. For the meningiomas, the probe panel was extended with a probe specific for chromosome 22. Loss of chromosome 22 was obvious in 21 of the 30 meningiomas, and was the sole abnormality in 11 meningiomas; in the other 10, this loss was associated with other chromosomal changes. Five of these tumors with additional aberrations were recurrent or atypical meningiomas. It is suggested that interphase cytogenetics can contribute to a better understanding of the biological behavior of these tumors and possibly result in better insights into prognosis and strategies for therapy.
Differences between human and mouse alpha‐fetoprotein expression during early development (2001)

Alpha-fetoprotein (AFP) is the major serum protein during development. AFP is one of the earliest proteins to be synthesised by the embryonic liver. The synthesis of AFP decreases dramatically after birth and only trace amounts are expressed in the adult liver. The tissue distribution of AFP in early human embryogenesis has not been defined. We have studied the expression pattern of AFP mRNA in human and mouse embryos by in situ hybridisation. In humans, AFP is expressed in the hepatic diverticulum at 26 d postovulation as it differentiates from the foregut endoderm (i.e. in the most primitive hepatocytes). It is also expressed in the endoderm of the gastrointestinal tract and in the yolk sac at this age. AFP is subsequently expressed in the mesonephros and transiently in the developing pancreas. In the mouse, no expression of AFP was observed in the mesonephros but other sites of expression were similar. Thus AFP has a distinct temporospatial expression pattern during the embryonic period and this differs between human and mouse species. It is interesting that AFP is expressed by tumours such as primitive gastrointestinal, renal cell and pancreatic tumours as well as those of hepatocyte origin. This distribution reflects the sites of AFP expression during development.
Rifampicin and isoniazid prophylactic chemotherapy for tuberculosis (1998)

Prophylaxis of tuberculosis in children with four month (n = 53) and three month regimens (n = 213) of rifampicin and isoniazid from 1987 to 1996 were tolerated without any toxicity. The reduction in the proportion of paediatric tuberculosis, which was seen after the introduction of chemoprophylaxis with longer regimens in 1981, was maintained with the shorter duration regimens. Altered immigration patterns and a fall in the proportion of infectious tuberculosis, as defined by sputum culture positivity, have been excluded as factors in the reduced paediatric proportion of tuberculosis. The data show such regimens have little toxicity and provide indirect evidence that three months chemoprophylaxis may be as effective as longer regimens.