gebhart/patrepeval huggingface dataset:
High‐throughput sequencing of TCR repertoires in multiple sclerosis reveals intrathecal enrichment of EBV‐reactive CD8+ T cells (2014)

Epstein-Barr virus (EBV) has long been suggested as a pathogen in multiple sclerosis (MS). Here, we used high-throughput sequencing to determine the diversity, compartmentalization, persistence, and EBV-reactivity of the T-cell receptor (TCR) repertoires in MS. TCR-β genes were sequenced in paired samples of cerebrospinal fluid (CSF) and blood from patients with MS and controls with other inflammatory neurological diseases. The TCR repertoires were highly diverse in both compartments and patient groups. Expanded T-cell clones, represented by TCR-β sequences >0.1%, were of different identity in CSF and blood of MS patients, and persisted for more than a year. Reference TCR-β libraries generated from peripheral blood T cells reactive against autologous EBV-transformed B cells were highly enriched for public EBV-specific sequences and were used to quantify EBV-reactive TCR-β sequences in CSF. TCR-β sequences of EBV-reactive CD8+ T cells, including several public EBV-specific sequences, were intrathecally enriched in MS patients only, whereas those of EBV-reactive CD4+ T cells were also enriched in CSF of controls. These data provide evidence for a clonally diverse, yet compartmentalized and persistent, intrathecal T-cell response in MS. The presented strategy links TCR sequence to intrathecal T-cell specificity, demonstrating enrichment of EBV-reactive CD8+ T cells in MS.
Quantum Chemical Study on Conformational Properties of Bipyridine Cardiotonics. (1993)

The conformational properties of bipyridine cardiotonics were investigated by means of quantum chemical (AM1(Austin Model 1)) calculations. The calculations for the tautomeric and ionic structures of 3, 4'-dipyridin-6(1H)-one (1), the basic structure for bipyridine cardiotonics, showed that the equilibrium conformations in the ionic structures are more planar than those in the neutral structures and that the rotational barrier of the cationic pyridone structure is characteristically higher compared to those of the pyridinol tautomer and 1'-hydro-3, 4'-bipyridinium cation. The difference in conformation between the well known cardiotonics, amrinone and milrinone, is more distinctive in the cationic structure, which is considered to be the usual structure in biological environments, than in the neutral structures.
The Biochemical and Neuroendocrine Bases of the Hyperalgesic Nocebo Effect (2006)

Despite the increasing research on placebos in recent times, little is known about the nocebo effect, a phenomenon that is opposite to the placebo effect and whereby expectations of symptom worsening play a crucial role. By studying experimental ischemic arm pain in healthy volunteers and by using a neuropharmacological approach, we found that verbally induced nocebo hyperalgesia was associated to hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis, as assessed by means of adrenocorticotropic hormone and cortisol plasma concentrations. Both nocebo hyperalgesia and HPA hyperactivity were antagonized by the benzodiazepine diazepam, suggesting that anxiety played a major role in these effects. The administration of the mixed cholecystokinin (CCK) type-A/B receptor antagonist proglumide blocked nocebo hyperalgesia completely but had no effect on HPA hyperactivity, which suggests a specific involvement of CCK in the hyperalgesic but not in the anxiety component of the nocebo effect. Importantly, both diazepam and proglumide did not show analgesic properties on basal pain, because they acted only on the nocebo-induced pain increase. These data indicate a close relationship between anxiety and nocebo hyperalgesia, in which the CCKergic systems play a key role in anxiety-induced hyperalgesia. These results, together with previous findings showing that placebo analgesia is mediated by endogenous opioids, suggest that the analgesic placebo/hyperalgesic nocebo phenomenon may involve the opposite activation of endogenous opioidergic and CCKergic systems.
Extensions to decision curve analysis, a novel method for evaluating diagnostic tests, prediction models and molecular markers (2008)

Decision curve analysis can be easily extended to many of the applications common to performance measures for prediction models. Software to implement decision curve analysis is provided.
Different effects of influenza virus, respiratory syncytial virus, and Sendai virus on human lymphocytes and macrophages (1982)

Influenza virus, respiratory syncytial virus, and Sendai virus depress human cell-mediated immune responses, such as mitogen-induced lymphocyte transformation, but differ in their ability to induce other immune defense mechanisms, such as interferon production. Exposure to the different viruses resulted in depressed transformation responses to the mitogen phytohemagglutinin by affecting the function of lymphocytes, or macrophages, or both cell types.
Interferon-dependent induction of mRNA for the major histocompatibility antigens in human fibroblasts and lymphoblastoid cells. (1982)

In human cells treated with interferons, there is an increase in the amount of HLA-A,B,C and beta 2-microglobulin exposed on the cell surface. We have used a cloned HLA-A,B,C cDNA probe to demonstrate by molecular hybridization that this effect of interferon is preceded by a large increase in the amount of HLA mRNA in the cell. This effect was found in five different human cell lines, with purified leukocyte and fibroblast interferons. The increase in HLA mRNA is comparable in its kinetics and dose-response to the induction of (2'-5') oligo(A) synthetase mRNA by interferons. Therefore, interferons seem to activate at least two cellular genes which have different biochemical functions.
Phylogenetic and Pathotypic Similarities betweenEscherichia coliIsolates from Urinary Tract Infections in Dogs and Extraintestinal Infections in Humans (2001)

Seventeen Escherichia coli isolates from dogs with urinary tract infection (UTI) were characterized with respect to phylogenetic background and virulence genotype and were compared with the E. coli reference (ECOR) collection and with human clinical isolates with similar serotypes from patients with diverse extraintestinal infections. Most of the canine urine isolates were from (virulence-associated) E. coli phylogenetic groups B2 or D, expressed papG allele III, and exhibited numerous other putative virulence genes that are characteristic of human extraintestinal pathogenic E. coli (ExPEC). Close phylogenetic and pathotypic correspondence was documented within 5 clonal groups among individual canine and human isolates, including archetypal human ExPEC strains CFT073 (O6:K2:H1), 536 (O6:K15:H31), and J96 (O4:K-:H5). These findings suggest that canine UTI isolates, rather than being dog-specific pathogens, as previously suspected, may pose an infectious threat to humans. Commonality between canine and human ExPEC has potentially important implications for disease prevention, antibiotic resistance avoidance, and studies of pathogenesis.
The Application of Near Infrared Spectroscopy for the Assessment of Avocado Quality Attributes (2012)

[Extract] Quality and safety evaluation of agricultural products has become an increasingly important consideration in market/commercial viability and systems for such evaluations are now demanded by customers, including distributors and retailers. Unfortunately, most horticultural products struggle with delivering adequate and consistent quality to the consumer. Removing inconsistencies and providing what the consumer expects is a key factor for retaining and expanding both domestic and international markets. Most commercial quality classification systems for fruit and vegetables are based on external features of the product, for example: shape, colour, size, weight and blemishes. However, the external appearance of most fruit is generally not an accurate guide to the internal or eating quality of the fruit. Internal quality of fruit is currently subjectively judged on attributes such as volatiles, firmness, and appearance. Destructive subjective measures such as internal flesh colour, or objective measures such as extraction of juice to measure sweetness (°Brix) or assessment of dry matter (DM) content are also used, although obviously not for every fruit – just a sample to represent the whole consignment.
Transparent Film Heater Using Single‐Walled Carbon Nanotubes (2007)

A transparent heater is produced from single-walled carbon nanotubes (SWCNTs) with a high thermal conductivity. A transparent conducting SWCNT film is fabricated on glass or polymer substrates by using a vacuum infiltration method. SWCNT films with a transparency of 65–97 % and a sheet resistance of 230–3500 Ω square–1 are demonstated. These films are good candidates for many applications that require transparent film heaters.
Organosilicon Reagents: Synthesis and Application to Palladium‐Catalyzed Cross‐Coupling Reactions (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
c-Myc Transforms Human Mammary Epithelial Cells through Repression of the Wnt Inhibitors DKK1 and SFRP1 (2007)

c-myc is frequently amplified in breast cancer; however, the mechanism of myc-induced mammary epithelial cell transformation has not been defined. We show that c-Myc induces a profound morphological transformation in human mammary epithelial cells and anchorage-independent growth. c-Myc suppresses the Wnt inhibitors DKK1 and SFRP1, and derepression of DKK1 or SFRP1 reduces Myc-dependent transforming activity. Myc-dependent repression of DKK1 and SFRP1 is accompanied by Wnt target gene activation and endogenous T-cell factor activity. Myc-induced mouse mammary tumors have repressed SFRP1 and increased expression of Wnt target genes. DKK1 and SFRP1 inhibit the transformed phenotype of breast cancer cell lines, and DKK1 inhibits tumor formation. We propose a positive feedback loop for activation of the c-myc and Wnt pathways in breast cancer.
Secreted Frizzled‐related proteins: searching for relationships and patterns (2002)

Secreted Frizzled-related proteins (SFRPs) are modulators of the intermeshing pathways in which signals are transduced by Wnt ligands through Frizzled (Fz) membrane receptors. The Wnt networks influence biological processes ranging from developmental cell fate, cell polarity and adhesion to tumorigenesis and apoptosis. In the five or six years since their discovery, the SFRPs have emerged as dynamically expressed proteins able to bind both Wnts and Fz, with distinctive structural properties in which cysteine-rich domains from Fz- and from netrin-like proteins are juxtaposed. The abundant expression of SFRP genes in the early embryo, altered expression patterns in disease states, and potential significance in the evolution of the vertebrate body plan, make these intriguing molecules relevant to investigations in diverse fields of biology and biomedical sciences.
Isolation and characterization of a temperature-sensitive mutant of Bombyx mori nucleopolyhedrovirus for a putative RNA polymerase gene. (1998)

Temperature-sensitive (ts) mutants of Bombyx mori nucleopolyhedrovirus (BmNPV), which exhibited no polyhedra formation at the non-permissive temperature of 33 degrees C, were produced using the base analogue 5-bromodeoxyuridine. A unique ts mutant, designated ts-S1, was characterized in terms of gene mutation and virulence in cultured cells and silkworm larvae. Mutant-infected BmN4 cells at 33 degrees C showed normal viral DNA synthesis but defective budded virus production and polyhedrin synthesis, suggesting the absence of late and very late gene expression. Silkworm larvae were injected with ts-S1 and reared at 33.5 degrees C. At 7 days post-injection, none of the larvae exhibited nucleopolyhedrosis but some possessed viral DNA, detected by PCR using virus-specific primers. Continued rearing of the larvae at a permissive temperature of 25 degrees C showed that, while most developed into normal adults, some developed nucleopolyhedrosis, indicating that the former larvae had aborted the virus infection during the course of rearing at 33.5 degrees C. No viral DNA was detected in the adults. Marker rescue tests to identify the lesion involved in the ts phenotype of ts-S1, and nucleotide sequencing of the identified genome region, showed a single nucleotide mutation of a putative RNA polymerase gene, late expression factor-8 (lef-8). These results indicate that lef-8 is essential for BmNPV replication in vitro and in vivo.
Oncostatin M Production and Regulation by Human Polymorphonuclear Neutrophils (1999)

Oncostatin M (OSM) is an interleukin-6 (IL-6) family cytokine known in particular to induce the synthesis of acute-phase proteins by hepatocytes. Because human polymorphonuclear neutrophils (PMN) can secrete numerous cytokines, the potential production of OSM by PMN was investigated. Highly purified PMN were found to contain an intracellular stock of preformed OSM that was rapidly mobilized by degranulating agents such as phorbol myristate acetate and granulocyte-macrophage colony-stimulating factor (GM-CSF). Moreover, PMN produced OSM after a few hours of stimulation by various agonists. The most potent effect was observed with the combination of lipopolysaccharide and GM-CSF, which had a concentration- and time-dependent effect at both the protein and mRNA levels. Actinomycin D strongly reduced OSM mRNA induction, suggesting the involvement of gene transcription. Cycloheximide inhibited OSM protein synthesis but did not affect the release of preformed stores. In addition, OSM production was downregulated by dexamethasone, whereas IL-10 had no effect. The OSM produced by PMN was biologically active, as demonstrated by its ability to induce 1-acid glycoprotein synthesis by HepG2 cells. OSM secretion thus occurs through a two-step mechanism in PMN, consisting of early release of a preformed stock, followed by de novo protein synthesis. This would allow rapid and sustained OSM release to occur at inflammatory sites, and may contribute to the modulation of local inflammation.
Chemical Characterization of a Family of Brain Lipids That Induce Sleep (1995)

A molecule isolated from the cerebrospinal fluid of sleep-deprived cats has been chemically characterized and identified as cis-9,10-octadecenoamide. Other fatty acid primary amides in addition to cis-9,10-octadecenoamide were identified as natural constituents of the cerebrospinal fluid of cat, rat, and human, indicating that these compounds compose a distinct family of brain lipids. Synthetic cis-9,10-octadecenoamide induced physiological sleep when injected into rats. Together, these results suggest that fatty acid primary amides may represent a previously unrecognized class of biological signaling molecules.
Antibodies against epididymal glycoproteins block fertilizing ability in rat (1984)

Antiserum against rat androgen-dependent secretory epididymal protein DE (raised in rabbit) was added to suspensions of rat spermatozoa from the cauda epididymidis which were used for artificial insemination. While control spermatozoa fertilized 41.6% of oocytes, those exposed to antiserum to protein DE fertilized only 6.6% (P less than 0.01). An equal amount of normal rabbit serum (NRS) did not cause inhibition (33.1%). To study the entry of antibodies into the epididymis, caudal tubules were cultured for 24 h and the fertility of the contained spermatozoa was assessed by artificial insemination. Culture in Medium 199 alone or with NRS resulted in spermatozoa which fertilized 52% of oocytes while the presence of antiserum to protein DE in the culture medium yielded spermatozoa which fertilized only 16.6% of oocytes (P less than 0.01). These results suggest (1) that the epididymal protein DE might be part of a sperm structure involved in the fertilization process, and (2) that, at least under the present culture conditions, immunoglobulins penetrate the epididymal epithelium in sufficient numbers to reduce fertility significantly.
The transformation of the media in East Germany since the Wende (1993)

(1993). The transformation of the media in East Germany since the Wende. Journal of Area Studies: Vol. 1, Perspectives on German Unification, pp. 25-36.
Effects of sitosterol and sitostanol on micellar solubility of cholesterol. (1989)

The influence of sitosterol and sitostanol on the solubility of cholesterol in mixed bile salt micelles in vitro and in vivo was investigated to examine the mechanism by which sitostanol inhibits cholesterol absorption more than does sitosterol. Both sitosterol and sitostanol decreased micellar solubility of cholesterol to a similar extent, when determined with the turbidity. Also, these sterols reduced the concentration of cholesterol in micelles, both in vitro and in vivo. The extent of the reduction of micellar solubility of cholesterol by these sterols was almost the same in vitro, whereas sitostanol tended to reduce the solubility more effectively than sitosterol in vivo. Thus, the interference with cholesterol solubilization in vivo may be responsible for effective inhibition of cholesterol absorption by sitostanol. Since the effect of sitostanol was not observed in vitro, there is a possibility that another factor(s) not included in the in vitro system might affect the action of sitostanol on micellar solubility of cholesterol in vivo.
Factors affecting fertilization of porcine oocytes following intracytoplasmic injection of sperm (2004)

The objective of this study was to optimize intracytoplasmic sperm injection (ICSI), and to assess the effects of membrane-damaged sperm on development of porcine oocytes following ICSI. For optimization of development following the ICSI process, sperm injected oocytes were activated 0.5-1.0 hr after ICSI with 1 x 30 micros pulse of 1.2, 1.7, 2.2, and 2.7 kV/cm DC in experiment 1. After 7-days of culture ICSI oocytes activated with [x1]2.2 kV/cm produced more blastocyts ([x2]34.4%, P < 0.05) than other treatment groups. In experiment 2, oocytes were activated with 1 x 30 micros pulse of 2.2 kV/cm at either 0, 1.5, 3, or 6 hr after ICSI. Oocytes activated 1.5 hr after [x3]ICSI yielded more blastocysts (27.6%)[M4] than in other treatments. In experiment 3, sperm were briefly exposed to 0.1% Triton X-100 to induce membrane damage. Live-dead staining of Percoll-sorted untreated spermatozoa (frozen-thawed) used in this study showed that over 96% were "alive" whereas none were "alive" after Triton X-100 treatment. The rate of development to blastocyst of oocytes injected with Triton X-100 treated sperm combined with electrical activation (EA) at 1 x 30 micros pulse of 2.2 kV/cm (EA, 40.0%) was the best, when compared with those injected with untreated sperm plus EA (P < 0.05). In experiment 4, the development rate of oocytes to the blastocyst stage ([x5]32.1%) following injection of a sperm head only was not significantly different from that of oocytes injected with whole sperm (31.0%). In conclusion, we found that an intact membrane and tail structures of pig spermatozoa are not essential for embryo development by ICSI, and furthermore, dead porcine spermatozoa, at an early stage of necrosis caused by plasma membrane damage, support better embryo development than do live non-damaged sperm.
The pediatric sepsis biomarker risk model: potential implications for sepsis therapy and biology (2014)

Sepsis remains a major cause of morbidity and mortality in adult and pediatric intensive care units. Heterogeneity of demographics, comorbidities, biological mechanisms, and severity of illness leads to difficulty in determining which patients are at highest risk of mortality. Determining mortality risk is important for weighing the potential benefits of more aggressive interventions and for deciding whom to enroll in clinical trials. Biomarkers can be used to parse patients into different risk categories and can outperform current methods of patient risk stratification based on physiologic parameters. Here we review the Pediatric Sepsis Biomarker Risk Model that has also been modified and applied to estimate mortality risk in adult patients. We compare the two models and speculate on the biological implications of the biomarkers in patients with sepsis.
Entraining Brain Oscillations to Influence Facial Perception (2015)

Relatively little is known about the role of brain oscillations in relation to cognitive function. While oscillations of all frequencies have be associated with most any neural process, no conclusive data has been found to support if oscillations are simply emergent or if they play a causal role in cognitive functions. To make headway on this problem, we employed entrainment, a technique used to synchronize brain oscillations. Entrainment was achieved by presenting subjects with alternating images of a neutral face and a scrambled face at 4 Hz such that the faces were presented at 2 Hz. After a few seconds of entrainment, a target image of either a face expressing happiness or disgust, or another scramble, was shown in-phase or out-of-phase of the entraining faces and followed by a masking image. Subjects were asked to identify if the target image was a scramble or a face, and if the face was expressing happiness or disgust. By monitoring neural activity with electroencephalography (EEG), we found that entrainment was successful. Oscillations in the occipital cortex were strongest around 4 Hz, and those in the parietal, central, and frontal cortices were strongest around 2 Hz. We also found that faces shown in-phase were easier to detect than those shown out-of-phase. Thus, initial results suggest entrainment can influence facial perception.
Stress-Induced Mutagenesis in Bacteria (2007)

Bacteria spend their lives buffeted by changing environmental conditions. To adapt to and survive these stresses, bacteria have global response systems that result in sweeping changes in gene expression and cellular metabolism. These responses are controlled by master regulators, which include: alternative sigma factors, such as RpoS and RpoH; small molecule effectors, such as ppGpp; gene repressors such as LexA; and, inorganic molecules, such as polyphosphate. The response pathways extensively overlap and are induced to various extents by the same environmental stresses. These stresses include nutritional deprivation, DNA damage, temperature shift, and exposure to antibiotics. All of these global stress responses include functions that can increase genetic variability. In particular, up-regulation and activation of error-prone DNA polymerases, down-regulation of error-correcting enzymes, and movement of mobile genetic elements are common features of several stress responses. The result is that under a variety of stressful conditions, bacteria are induced for genetic change. This transient mutator state may be important for adaptive evolution.
A gene activated by growth factors is related to the oncogene v-jun. (1988)

We have recently identified by cDNA cloning a set of genes that are rapidly activated in cultured mouse cells by protein growth factors. Here we report that the nucleotide sequence of a cDNA (clone 465) derived from one of these immediate early genes (hereafter called jun-B) encodes a protein homologous to that encoded by the avian sarcoma virus 17 oncogene v-jun. Homology between the jun-B and v-jun proteins is in two regions: one near the N terminus and the other at the C terminus. The latter sequence was shown by Vogt et al. [Vogt, P. K., Bos, T. J. & Doolittle, R. F. (1987) Proc. Natl. Acad. Sci. USA 84, 3316-3319] to have regions of sequence similarity to the DNA-binding domain of the yeast transcriptional regulatory protein GCN4 and to the oncogenic protein fos. Southern blots of human, mouse, and chicken DNA demonstrate that jun-B and c-jun are different genes and that there may be other vertebrate genes related to jun-B and c-jun. These findings suggest that there is a jun family of genes encoding related transcriptional regulatory proteins. The jun-B protein, and perhaps other members of the jun family, may play a role in regulating the genomic response to growth factors.