gebhart/patrepeval huggingface dataset:
Cloning and Heterologous Expression of an α1,3-Fucosyltransferase Gene from the Gastric PathogenHelicobacter pylori (1997)

Helicobacter pylori is an important human pathogen which causes both gastric and duodenal ulcers and is also associated with gastric cancer and lymphoma. This microorganism has been shown to express cell surface glycoconjugates including Lewis X (Lex) and Lewis Y. These bacterial oligosaccharides are structurally similar to tumor-associated carbohydrate antigens found in mammals. In this study, we report the cloning of a novel alpha1,3-fucosyltransferase gene (HpfucT) involved in the biosynthesis of Lex within H. pylori. The deduced amino acid sequence of HpfucT consists of 478 residues with the calculated molecular mass of 56,194 daltons, which is approximately 100 amino acids longer than known mammalian alpha1,3/1,4-fucosyltransferases. The approximately 52-kDa protein encoded by HpfucT was expressed in Escherichia coli CSRDE3 cells and gave rise to alpha1,3-fucosyltransferase activity but neither alpha1,4-fucosyltransferase nor alpha1,2-fucosyltransferase activity as characterized by radiochemical assays and capillary zone electrophoresis. Truncation of the C-terminal 100 amino acids of HpFuc-T abolished the enzyme activity. An approximately 72-amino acid region of HpFuc-T exhibits significant sequence identity (40-45%) with the highly conserved C-terminal catalytic domain among known mammalian and chicken alpha1,3-fucosyltransferases. These lines of evidence indicate that the HpFuc-T represents the bacterial alpha1,3-fucosyltransferase. In addition, several structural features unique to HpFuc-T, including 10 direct repeats of seven amino acids and the lack of the transmembrane segment typical for known eukaryotic alpha1,3-fucosyltransferases, were revealed. Notably, the repeat region contains a leucine zipper motif previously demonstrated to be responsible for dimerization of various basic region-leucine zipper proteins, suggesting that the HpFuc-T protein could form dimers.
Haematopoietic stem cell transplantation in haemophagocytic lymphohistiocytosis (2005)

Haemophagocytic lymphohistiocytosis (HLH) poses major therapeutic challenges, and the primary inherited form, familial haemophagocytic lymphohistiocytosis (FHL), is usually fatal. We evaluated, including Cox regression analysis, survival in 86 children (29 familial) that received HLH-94-therapy (etoposide, dexamethasone, ciclosporin) followed by allogeneic stem cell transplantation (SCT) between 1995 and 2000. The overall estimated 3-year-survival post-SCT was 64% [confidence interval (CI) = +/-10%] (n = 86); 71 +/- 18% in those patients with a matched related donor (MRD, n = 24), 70 +/- 16% with a matched unrelated donor (MUD, n = 33), 50 +/- 24% with a family haploidentical donor (haploidentical, n = 16), and 54 +/- 27% with a mismatched unrelated donor (MMUD, n = 13). After adjustment for potential confounding factors, estimated odds ratios (OR) for mortality were 1.93 (CI =0.61-6.19) for MUD, 3.31 (1.02-10.76) for haploidentical, and 3.01 (0.91-9.97) for MMUD, compared with MRD. In children with active disease after 2-months of therapy (n = 43) the OR was 2.75 (1.26-5.99), compared with inactive disease (n = 43). In children with active disease at SCT (n = 37), the OR was 1.80 (0.80-4.06) compared with inactive disease (n = 49), after adjustment for disease activity at 2-months. Mortality was predominantly transplant-related. Most HLH patients survived SCT using MRD or MUD, and survival with partially mismatched donors was also acceptable. Patients that responded well to initial pretransplant-induction therapy fared best, but some persisting HLH activity should not automatically preclude performing SCT.
The HMM-based speech synthesis system (HTS) version 2.0. (2007)

A statistical parametric speech synthesis system based on hidden Markov models (HMMs) has grown in popularity over the last few years. This system simultaneously models spectrum, excitation, and duration of speech using context-dependent HMMs and generates speech waveforms from the HMMs themselves. Since December 2002, we have publicly released an open-source software toolkit named HMM-based speech synthesis system (HTS) to provide a research and development platform for the speech synthesis community. In December 2006, HTS version 2.0 was released. This version includes a number of new features which are useful for both speech synthesis researchers and developers. This paper describes HTS version 2.0 in detail, as well as future release plans.
Primary Biliary Cirrhosis (2005)

Primary biliary cirrhosis, a slowly progressive autoimmune liver disease characterized by portal inflammation and an immune-mediated destruction of the intrahepatic bile ducts, leads to decreased bile secretion and the retention of toxic substances within the liver. This review considers new data concerning both the autoimmune responses involved and the treatment of primary biliary cirrhosis.
MicroRNA-33b Inhibits Breast Cancer Metastasis by Targeting HMGA2, SALL4 and Twist1 (2015)

MicroRNAs are a class of small noncoding RNAs that regulate gene expression post-transcriptionally either by inhibiting protein translation or by causing the degradation of target mRNAs. Current evidence indicates that miR-33b is involved in the regulation of lipid metabolism, cholesterol homeostasis, glucose metabolism and several human diseases; however, whether miR-33b contributes to the pathogenesis of human cancers and participates in the regulation of self-renewal of human cancer stem cells remains unknown. Here, we report the identification of miR-33b as a negative regulator of cell stemness and metastasis in breast cancer. Compared with paired normal breast tissues, miR-33b expression is downregulated in breast tumor samples and is inversely correlated with lymph node metastatic status. Ectopic overexpression of miR-33b in highly metastatic breast cancer cells suppresses cell self-renewal, migration and invasion in vitro and inhibits lung metastasis in vivo. Conversely, miR-33b knockdown promotes the self-renewal, migration and invasion capabilities of noncancerous mammary epithelial cells. The mechanism through which miR-33b inhibits the stemness, migration and invasion of breast cancer cells is by targeting HMGA2, SALL4 and Twist1. These data indicate that miR-33b acts as an onco-suppressive microRNA in breast cancer progression by inhibiting the stemness and metastasis of breast cancer cells.
Thromboxane Inhibitors Attenuate Inflammatory and Fibrotic Changes in Rat Liver Despite Continued Ethanol Administrations (2012)

Thromboxane inhibitors attenuated the alcoholic liver injury, inflammation and fibrotic changes despite continued EtOH administration. Inhibition of the production of thromboxane by thromboxane inhibitor and receptor antagonists may be a useful treatment strategy in clinical alcoholic liver disease.
Type IIA Procollagen Amino Propeptide Is Localized in Human Embryonic Tissues (1997)

Type II procollagen is synthesized in two forms generated by the alternative splicing of its precursor mRNA. The alternatively spliced domain, exon 2, encodes the 69-amino-acid cysteine-rich region of the NH2 propeptide. Studies of mRNA expression have shown that the longer form, designated Type IIA procollagen, is synthesized by chondroprogenitor cells and various noncartilaginous tissues. The shorter form, Type IIB procollagen, is synthesized by differentiated chondrocytes. As the initial step in our investigations of the function of the Type IIA procollagen, the protein domain corresponding to exon 2 was created as a recombinant fusion protein and used to raise antibodies in rabbits. The resulting antiserum was specific for Type IIA procollagen NH2 propeptide as shown by ELISA, Western blotting, and immunofluorescent co-localization with the triple-helical domain of Type II collagen. Type IIA procollagen was identified in tissue culture medium of 54-day human fetal ribs. Confocal microscopy was used to localize the Type IIA NH2 propeptide in Day 50 and 53 human embryos. In the digital rays of the developing hand, where only Type IIA procollagen mRNA was detected, Type IIA procollagen NH2 propeptide was observed in the extracellular matrix. The presence of Type IIA procollagen NH2 propeptide was observed in the cartilage of the developing long bones of the lower arm and vertebral bodies even though these tissues synthesize Type IIB mRNA at this developmental stage. Type IIA procollagen NH2 propeptide was localized in the developing trachea, a cartilage that does not undergo endochondral bone formation. Type IIA NH2 propeptide was also localized in noncartilaginous tissues known to synthesize Type IIA mRNA, such as the intervertebral area, perichondrium, notochordal sheath, and neuroepithelium of the otic vesicle. In most tissues, co-localization with antiserum against the triple-helical domain of Type II collagen was observed. Positive immunoreactivity with the Type IIA NH2 propeptide antiserum indicates, for the first time, that this propeptide is present in the tissue. Co-localization of NH2 propeptide antibodies with the triple-helical domain of the collagen molecule suggests that Type IIA procollagen is intact in the extracellular matrix of these tissues. Taken together, these results strongly suggest that around cells that synthesize Type IIA procollagen mRNA, Type IIA procollagen NH2 propeptide is secreted and deposited into the extracellular matrix. In light of these results, we predict that Type IIA procollagen plays a role in differentiation of tissues that augments its purely architectural function.
Strategies for Drug Delivery to The Human Inner Ear by Multifunctional Nanoparticles (2011)

This finding raises hope in terms of future multifunctional NP-based drug delivery strategy to the human inner ear.
Autosomal dominant adult neuronal ceroid lipofuscinosis: Parkinsonism due to both striatal and nigral dysfunction (2002)

We describe a family with adult neuronal ceroid lipofuscinosis, with apparent autosomal dominant inheritance, observed in six affected individuals in three generations. Disease onset was usually in the fifth decade, but was earlier in the youngest generation. Early symptoms consisted of myoclonus in face and arms, epilepsy, auditory symptoms, cognitive decline, or depression. Parkinsonism occurred a few years after disease onset, with stooped posture, shuffling gait, bradykinesia, and mask face. Four subjects deteriorated to a state of severe handicap, with severe dementia, contractures, dysphagia, and dysarthria. Leg weakness evolved to flaccid paraparesis in two patients. Diagnosis was confirmed by brain biopsy in one patient and full autopsy in two patients. Abundant intraneuronal storage of autofluorescent material was found throughout the brain. Electron microscopy showed granular osmiophilic deposits and scarce fingerprint profiles. Striking loss of neurons in the substantia nigra pars compacta and reticulata was found. (123)I-IBZM Single photon emission computed tomography in two patients showed loss of postsynaptic D2 receptor binding in the striatum. We conclude that parkinsonism in ANCL is likely to be caused by both presynaptic nigral cell loss and postsynaptic striatal degeneration.
The RiceYABBY1Gene Is Involved in the Feedback Regulation of Gibberellin Metabolism (2007)

Gibberellin (GA) biosynthesis is regulated by feedback control providing a mechanism for GA homeostasis in plants. However, regulatory elements involved in the feedback control are not known. In this report, we show that a rice (Oryza sativa) YABBY1 (YAB1) gene had a similar expression pattern as key rice GA biosynthetic genes GA3ox2 and GA20ox2. Overexpression of YAB1 in transgenic rice resulted in a semidwarf phenotype that could be fully rescued by applied GA. Quantification of the endogenous GA content revealed increases of GA(20) and decreases of GA(1) levels in the overexpression plants, in which the transcripts of the biosynthetic gene GA3ox2 were decreased. Cosuppression of YAB1 in transgenic plants induced expression of GA3ox2. The repression of GA3ox2 could be obtained upon treatment by dexamethasone of transgenic plants expressing a YAB1-glucocorticoid receptor fusion. Importantly, we show that YAB1 bound to a GA-responsive element within the GA3ox2 promoter. In addition, the expression of YAB1 was deregulated in GA biosynthesis and signaling mutants and could be either transiently induced by GA or repressed by a GA inhibitor. Finally, either overexpression or cosuppression of YAB1 impaired GA-mediated repression of GA3ox2. These data together suggest that YAB1 is involved in the feedback regulation of GA biosynthesis in rice.
The Cells and Circuitry for Itch Responses in Mice (2013)

Itch is triggered by somatosensory neurons expressing the ion channel TRPV1 (transient receptor potential cation channel subfamily V member 1), but the mechanisms underlying this nociceptive response remain poorly understood. Here, we show that the neuropeptide natriuretic polypeptide b (Nppb) is expressed in a subset of TRPV1 neurons and found that Nppb(-/-) mice selectively lose almost all behavioral responses to itch-inducing agents. Nppb triggered potent scratching when injected intrathecally in wild-type and Nppb(-/-) mice, showing that this neuropeptide evokes itch when released from somatosensory neurons. Itch responses were blocked by toxin-mediated ablation of Nppb-receptor-expressing cells, but a second neuropeptide, gastrin-releasing peptide, still induced strong responses in the toxin-treated animals. Thus, our results define the primary pruriceptive neurons, characterize Nppb as an itch-selective neuropeptide, and reveal the next two stages of this dedicated neuronal pathway.
A circular trans-acting hepatitis delta virus ribozyme (1993)

A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of the 5' and 3' splice sites, flanking the single HDV-like ribozyme sequence-containing exon, is reversed. Trans-cleavage activity of the circular HDV-like ribozyme was comparable to linear permutations of HDV ribozymes containing the same core sequence, and was shown not to be due to linear contaminants in the circular ribozyme preparation. In nuclear and cytoplasmic extracts from HeLa cells, the circular ribozyme had enhanced resistance to nuclease degradation relative to a linear form of the ribozyme, suggesting that circularization may be a viable alternative to chemical modification as a means of stabilizing ribozymes against nuclease degradation.
The BRENDA enzyme information system–From a database to an expert system (2017)

Enzymes, representing the largest and by far most complex group of proteins, play an essential role in all processes of life, including metabolism, gene expression, cell division, the immune system, and others. Their function, also connected to most diseases or stress control makes them interesting targets for research and applications in biotechnology, medical treatments, or diagnosis. Their functional parameters and other properties are collected, integrated, and made available to the scientific community in the BRaunschweig ENzyme DAtabase (BRENDA). In the last 30 years BRENDA has developed into one of the most highly used biological databases worldwide. The data contents, the process of data acquisition, data integration and control, the ways to access the data, and visualizations provided by the website are described and discussed.
Recent trends in durum wheat milling and pasta processing: impact on durum wheat quality requirements (2001)

Durum wheat quality criteria continually evolve in response to market pressure and consumer preference. Increasing demand for specific durum wheat quality attributes for different end-products requires development of more rapid objective means to grade and classify wheat parcels on the basis of processing potential. Near-infrared spectroscopy and image analysis have considerable potential for rapid objective wheat grading and classification. Preprocessing (debranning before milling) enhances durum wheat milling performance. Surface discolourations, major factors in grading durum wheat because of negative impact on semolina colour and presence of visible specks, will become less important if preprocessing becomes more accepted by durum wheat millers. Semolina granulation has become finer to accommodate large high capacity pasta presses and Polymatik presses. The move to finer granulation, particularly when protein content is specified, makes hard vitreous kernel content of less importance to durum wheat millers. Intense competition in the pasta industry has made pasta colour, an important aesthetic factor in consumer choice, more universally important. That, combined with a trend to higher semolina extraction rates, will require plant breeders to develop durum wheat varieties with higher levels of yellow pigment and lower levels of oxidative enzymes. High temperature (HT) and ultra-high temperature (UHT) drying have become the processes of choice for most pasta manufacturers. Strong gluten is likely to remain an important specification in some markets even though it appears to have less influence on cooking quality for HT and UHT pasta that for low temperature-dried pasta. Regardless of drying temperature, protein content will continue to be a fundamental requirement to ensure good pasta cooking quality. There is increasing interest in using durum wheat for baking. Durum wheat baking quality does not appear to be linked to pasta cooking quality, giving hope for development of durum wheat varieties suitable for both pasta-making and bread-making.
THE ROLE OF RESPIRATION AND PHOTOSYNTHESIS IN THE CHLOROPLAST REGENERATION IN THE “GLUCOSE-BLEACHED” CELLS OF CHLORELLA PROTOTHECOIDES (1966)

1. As previously demonstrated, entirely chlorophyll-less cells of Chlorella protothecoides are obtained when the alga is grown in a medium rich in glucose and poor in nitrogen source (urea). These cells, which are referred to as “glucose-bleached” cells, have neither discernible chloroplast structures nor photosynthetic activity. When the “glucose-bleached” cells are incubated, in the light, in a nitrogen-enriched mineral medium without added glucose, they turn green, after an induction period, with regeneration of chloroplasts and development of the capacity for performing normal photosynthesis. In the present study, changes in respiratory activity of algal cells during the process of greening (chloroplast regeneration) were followed, and the effects of various inhibitors of respiration and photosynthesis on the greening process were examined. 2. The glucose-bleached cells showed a very low activity of respiration, and the activity increased markedly during an early phase of chloroplast regeneration, showing, however, a decrease during the subsequent phase of greening. 3. Some antimetabolites which inhibited the cell respiration, were found to suppress also the greening of cells. 2,4-Dinitrophenol and azide, potent inhibitors of oxidative phosphorylation, accelerated considerably both the respiration and greening of algal cells. CMU inhibited completely photosynthesis of the greening cells, but suppressed only slightly the greening process. 4. Based on these results it was concluded that the primary role of respiration in the chloroplast regeneration in the glucose-bleached cells is to produce oxidized carbon compounds (and perhaps reduced forms of NAD and NADP) for various biosynthetic reactions. It was further suggested that ATP may be supplied for the chloroplast regeneration by a certain means different from the oxidative phosphorylation or photophosphorylation. The activities of photosynthetic phosphorylation and CO2-fixation developing in the greening cells do not appear to play any essential role in the chloroplast regeneration.
Exercise-induced malignant hyperthermia in an English Springer Spaniel (1987)

An exercise-induced malignant hyperthermia-like syndrome developed in an English Springer Spaniel. Moderate exercise resulted in pronounced hyperlactacidemia, dyspnea, and hyperthermia. Before exercise, the dog had high activities of serum muscle enzymes, mild reticulocytosis, abnormally increased erythrocyte osmotic fragility, and a positive result from the caffeine-halothane contracture test. This report supports the hypothesis of a canine stress syndrome and indicates a role for exercise/challenge tests in diagnosis of malignant hyperthermia susceptibility.
Fluorescence <I>In Situ</I> Hybridization: <I>Technical Overview<I> (2004)

Fluorescence in situ hybridization (FISH) is now widely applied to the detection of specific normal and aberrant DNA sequences in both intact cells, either in interphase or metaphase, and isolated chromosomes. A logical extension of early in situ hybridization (ISH) techniques, simply exploiting the ability to label DNA with high-energy fluorophores, FISH is now applied in an increasing number of molecular diagnostic areas, including karyotype analysis, gene mapping, disease diagnosis, and therapeutic targeting. FISH has advantages over ISH, which are critical to its implementation in diagnostic medicine, particularly in reduced exposure time over radioactive ISH methods. Furthermore, FISH is perceived to be safer and has the added advantage that multiple fluorochromes can be used to discriminate different targets simultaneously.
Antitumor activity of a homing peptide that targets tumor lymphatics and tumor cells (2004)

LyP-1 is a peptide selected from a phage-displayed peptide library that specifically binds to tumor and endothelial cells of tumor lymphatics in certain tumors. Fluorescein-conjugated LyP-1 and a related peptide, LyP-1b, strongly accumulated in primary MDA-MB-435 breast cancer xenografts and their metastases from i.v. peptide injections, allowing visualization of orthotopic tumors in intact mice. The LyP peptide accumulation coincided with hypoxic areas in tumors. LyP-1 induced cell death in cultured human breast carcinoma cells that bind and internalize the peptide. Melanoma cells that do not bind LyP-1 were unaffected. Systemic LyP-1 peptide treatment of mice with xenografted tumors induced with the breast cancer cells inhibited tumor growth. The treated tumors contained foci of apoptotic cells and were essentially devoid of lymphatics. These results reveal an unexpected antitumor effect by the LyP-1 peptide that seems to be dependent on a proapoptotic/cytotoxic activity of the peptide. As LyP-1 affects the poorly vascularized tumor compartment, it may complement treatments directed at tumor blood vessels.