gebhart/patrepeval huggingface dataset:
TFF2/SP-deficient mice show decreased gastric proliferation, increased acid secretion, and increased susceptibility to NSAID injury (2002)

Trefoil factor family 2 (TFF2), also known as spasmolytic polypeptide, is a member of the trefoil family of peptides and is expressed primarily in the mucous neck cells of the gastric mucosa. To study the physiologic role of TFF2, we have generated TFF2-deficient mice through targeted gene disruption. Homozygous mutant mice were viable and fertile without obvious gastrointestinal abnormalities. However, quantitative measurements revealed a significant decrease in gastric mucosal thickness and in gastric mucosal proliferation rates. In addition, there was a twofold increase in activated parietal cells resulting in a twofold increase in basal and stimulated gastric acid output and an undetectable serum gastrin level. The TFF2-deficient mice also showed a significant increase in the degree of gastric ulceration after administration of indomethacin. Taken together, these results suggest a physiologic role for TFF2 to promote mucosal healing through the stimulation of proliferation and downregulation of gastric acid secretion.
Kaposi sarcoma–associated viral cyclin K overrides cell growth inhibition mediated by oncostatin M through STAT3 inhibition (2003)

DNA viruses have evolved a number of mechanisms to inhibit the major cellular tumor-suppressor pathways. Viral oncogenes can override growth suppressive signals and extend the virus proliferative capacity. The Kaposi sarcoma-associated human herpesvirus 8 (KSHV) encodes a protein, cyclin K, that is similar to cellular cyclin D1 but behaves atypically. Cyclin K resists the actions of the p16 INK4a and p27Kip1 inhibitors and extends the range of cdk6 substrates, thereby inducing cell-cycle progression toward S phase. In this study, we show that cyclin K overrides growth suppressive signals through signal transducer and activator of transcription 3 (STAT3) inactivation. Cyclin K was found to associate with the activation domain of STAT3 to inhibit its DNA-binding and transcriptional activities. Overexpression of cyclin K and inhibition of STAT3 prevents the growth suppressive effect imposed by the interleukin 6-type cytokine, oncostatin M. Altogether, these results suggest that KSHV is able to override growth suppressive effects through multiple mechanisms, and they further indicate that cyclin K plays an important role in the oncogenic activity of these viruses.
Identification of genes with abnormal expression changes in acute myeloid leukemia (2007)

Acute myeloid leukemia (AML) is one of the most common and deadly forms of hematopoietic malignancies. We hypothesized that microarray studies could identify previously unrecognized expression changes that occur only in AML blasts. We were particularly interested in those genes with increased expression in AML, believing that these genes may be potential therapeutic targets. To test this hypothesis, we compared gene expression profiles between normal hematopoietic cells from 38 healthy donors and leukemic blasts from 26 AML patients. Normal hematopoietic samples included CD34+ selected cells (N = 18), unselected bone marrows (N = 10), and unselected peripheral bloods (N = 10). Twenty genes displayed AML-specific expression changes that were not found in the normal hematopoietic cells. Subsequent analyses using microarray data from 285 additional AML patients confirmed expression changes for 13 of the 20 genes. Seven genes (BIK, CCNA1, FUT4, IL3RA, HOMER3, JAG1, WT1) displayed increased expression in AML, while 6 genes (ALDHA1A, PELO, PLXNC1, PRUNE, SERPINB9, TRIB2) displayed decreased expression. Quantitative RT/PCR studies for the 7 over-expressed genes were performed in an independent set of 9 normal and 21 pediatric AML samples. All 7 over-expressed genes displayed an increased expression in the AML samples compared to normals. Three of the 7 over-expressed genes (WT1, CCNA1, and IL3RA) have already been linked to leukemogenesis and/or AML prognosis, while little is known about the role of the other 4 over-expressed genes in AML. Future studies will determine their potential role in leukemogenesis and their clinical significance.
Adenosine stimulates proliferation of human endothelial cells in culture (1993)

The effect of adenosine on proliferation of human endothelial cells was investigated by adding adenosine to the medium of cultures derived from human umbilical veins. Cell counts on cultures grown in 10 microM adenosine for 4-7 days were 41-53% greater than counts from control cultures. In contrast, 10 microM adenosine had no effect on growth of a human fibroblast cell strain (IMR-90). Neither inosine nor 2',5'-dideoxyadenosine influenced endothelial cell growth at concentrations of 0.1 or 10 microM. Addition of adenosine deaminase abolished the proliferative effect of added adenosine and inhibited proliferation by 16% in control cultures, suggesting that endogenous adenosine may enhance proliferation in culture. The adenosine receptor antagonist, 8-phenyltheophylline, at 0.1 and 1.0 microM blocked the enhanced proliferation caused by 10 microM adenosine. Addition of 10 microM adenosine enhanced DNA synthesis in endothelial cell cultures as indicated by an increased incorporation of [3H]thymidine into acid-insoluble cell material. The results indicate that addition of physiological concentrations of adenosine to human umbilical vein endothelial cell cultures stimulates proliferation, possibly via a surface receptor, and suggest that adenosine may be a factor for human endothelial cell growth and possibly angiogenesis.
Protein and antigen profiles of prevalent serovars of Leptospira interrogans (1991)

Whole-cell and detergent-soluble proteins, enriched for outer membrane antigens, of the Leptospira interrogans serovars present in commercially available pentavalent vaccines (hardjo, pomona, icterohaemorrhagiae, grippotyphosa, and canicola) were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting (immunoblotting). Protein and antigenic profiles of these serovars, representing several serogroups, were compared with similar profiles of the most common North American bovine pathogen, serovar hardjo type hardjo bovis. The reference strain of serovar balcanica and a hardjoprajitno bovine field isolate (serovar hardjo) were also assayed. Coomassie blue-stained gels revealed extensive protein similarities, and Western blots demonstrated antigenic relatedness throughout the low- and high-molecular-weight regions. Possible quantitative differences in protein expression among the strains were noted, as were similarities in the protein profiles of type hardjo bovis and the balcanica reference strain. A cocktail composed of these homologous antigens may serve as an efficacious subunit vaccine for leptospirosis.
Activity of selective fully human agonistic antibodies to the TRAIL death receptors TRAIL‐R1 and TRAIL‐R2 in primary and cultured lymphoma cells: induction of apoptosis and enhancement of doxorubicin‐ and bortezomib‐induced cell death (2005)

Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL/Apo2L) is a death protein that preferentially kills tumour cells while sparing normal cells. TRAIL has four exclusive receptors, two of which (TRAIL-R1, TRAIL-R2) are death receptors. Both TRAIL/Apo2L and agonistic antibodies to the TRAIL death receptors are currently being explored for cancer therapy. Although the activity of TRAIL/Apo2L in a variety of haematological malignancies has been examined, the activity of anti-TRAIL receptor agonistic antibodies in primary and cultured lymphoma cells has not. Using two fully human selective agonistic monoclonal antibodies to the TRAIL death receptors TRAIL-R1 (HGS-ETR1) and TRAIL-R2 (HGS-ETR2) this study demonstrated that both monoclonal antibodies activated caspase-8 and induced cell death in five of nine human lymphoma cell lines, and induced >10% cell death in 67% and 70%, respectively, of 27 primary lymphoma cells, and >20% cell death in at least one-thirds of the samples. HGS-ETR1 and HGS-ETR2 demonstrated comparable activity in the fresh tumour samples, which was independent of TRAIL receptor surface expression, Bax, cFLIP, or procaspase-8 expression, or exposure to prior therapy. Furthermore, both antibodies enhanced the killing effect of doxorubicin and bortezomib. Our data demonstrate that HGS-ETR1 and HGS-ETR2 monoclonal antibodies can induce cell death in a variety of cultured and primary lymphoma cells, and may have therapeutic value in lymphoma.
Amino acid sequences that determine the nuclear localization of yeast histone 2B. (1987)

Histone-beta-galactosidase protein fusions were used to identify the domain of yeast histone 2B, which targets this protein to the nucleus. Amino acids 28 to 33 in H2B were required for nuclear localization of such fusion proteins and thus constitute a nuclear localization sequence. The amino acid sequence in this region (Gly-29 Lys Lys Arg Ser Lys Ala) is similar to the nuclear location signal in simian virus 40 large T antigen (Pro-126 Lys Lys Lys Arg Lys Val) (D. Kalderon, B.L. Roberts, W.D. Richardson, and A.E. Smith, Cell 39:499-509, 1984). A point mutation changing lysine 31 to methionine abolished nuclear localization of an H2B-beta-galactosidase fusion protein containing amino acids 1 to 33 of H2B. However, an H2B-beta-galactosidase fusion protein containing both this point mutation and the H2A interaction domain of H2B was nuclear localized. These results suggest that H2A and H2B may be cotransported to the nucleus as a heterodimer.
Evaluation of Pancreatic Cancer Clinical Trials and Benchmarks for Clinically Meaningful Future Trials (2016)

Applying the benchmark of a 50% improvement in overall survival as the primary end point to phase 2 data, or secondary end points of a 90% increase in 1-year survival or an 80% to 100% increase in progression-free survival, showed the greatest ability to predict a clinically meaningful phase 3 trial. Had these criteria been applied to these trials over the past 25 years, more than 11 571 patients enrolled in phase 3 trials that did not meet the primary end point could theoretically have been diverted to earlier-stage trials in an attempt to more rapidly advance the field.
A new efficient verifiable fuzzy keyword search scheme (2012)

As cloud computing becomes prevalent, more and more sensitive data is being centralized into the cloud by users. To maintain the confidentiality of sensitive user data against untrusted servers, the data should be encrypted before they are uploaded. However, this raises a new challenge for performing search over the encrypted data efficiently. Although the existing searchable encryption schemes allow a user to search the encrypted data with confidentiality, these solutions cannot support the verifiability of searching result. We argue that a cloud server may be selfish in order to save its computation ability or bandwidth. For example, it may execute only a fraction of the search and returns part of the searching result. In this paper, we propose a new verifiable fuzzy keyword search scheme based on the symbol-tree which not only supports the fuzzy keyword search, but also enjoys the verifiability of the searching result. Through rigorous security and efficiency analysis, we show that our proposed scheme is secure under the proposed model, while correctly and efficiently realizing the verifiable fuzzy keyword search.
Synthesis and Study of Thiocarbonate Derivatives of Choline as Potential Inhibitors of Acetylcholinesterase (1997)

Fourteen alkyl and aryl thiocarbonate derivatives of choline were synthesized and studied as potential inhibitors of acetylcholinesterase (AChE). Twelve of the compounds inhibited AChEs derived from calf forebrain, human red blood cells, and octopus brain ranging from low to moderately high inhibition potency. The concentration of each inhibitory compound giving 50% inhibition of enzyme activity (IC50 values, which ranged from 1 x 10(-2) to 8 x 10(-7) M) was determined and is reported; inhibitor constants (Ki values) for the most inhibitory compounds, (1-pentylthiocarbonyl)choline chloride and (1-heptylthiocarbonyl)choline chloride, were calculated from kinetic data and are also reported. The inhibitors are competitive with substrate, and they are not hydrolyzed by the AChE activities. Certain of these new compounds may provide direction for the development of new drugs that have anticholinesterase activity and may be used for the treatment of Alzheimer's disease.
Synthetic Antimicrobial Peptide Design (1995)

To guide the design of potential plant pathogen-resistance genes, synthetic variants of naturally occurring antimicrobial gene products were evaluated. Five 20-amino acid (ESF1, ESF4, ESF5, ESF6, ESF13), one 18-amino acid (ESF12), and one 17-amino acid (ESF17) amphipathic peptide sequences were designed, synthesized, and tested with in vitro bioassays. Positive charges on the hydrophilic side of the peptide were shown to be essential for antifungal activity, yet the number of positive charges could be varied with little or no change in activity. The size could be reduced to 18 amino acids, but at 17 amino acids a significant reduction in activity was observed. ESF1, 5, 6, and 12 peptides were inhibitory to the germination of conidia from Cryphonectria parasitica, Fusarium oxysporum f. sp. lycopersici, and Septoria musiva but did not inhibit the germination of pollen from Castanea mollissima and Salix lucida. ESF12 also had no effect on the germination of Malus sylvestris and Lycopersicon esculentum pollen, but inhibited the growth of the bacteria Agrobacterium tumefaciens, Erwinia amylovora, and Pseudomonas syringae. The minimal inhibitory concentrations of the active ESF peptides were similar to those of the naturally occurring control peptides, magainin II and cecropin B. The significant differential in sensitivity between the microbes and plant cells indicated that the active ESF peptides are potentially useful models for designing plant pathogen-resistance genes.
Selective stimulation of glucagon secretion by β2‐adrenoceptors in isolated islets of Langerhans of the rat (1991)

1. In rat isolated islets of Langerhans the selective beta 2-adrenoceptor agonist, clenbuterol (1 to 20 microM), significantly increased the level of adenosine 3':5'-cyclic monophosphate (cyclic AMP) within 2 min of incubation. 2. The cyclic AMP response to clenbuterol was inhibited in the presence of the selective beta 2 adrenoceptor antagonist, ICI 118551 (0.1 or 10 microM) but remained unchanged when the beta 1-antagonist, atenolol (0.1 microM) was administered. 3. Despite causing an elevation in cyclic AMP, clenbuterol (up to 20 microM) failed to influence insulin secretion at any glucose concentration tested, even in the presence of a phosphodiesterase inhibitor. 4. By contrast, clenbuterol elicited a dose-dependent rise in the rate of glucagon secretion; the maximal agonist-induced increase in secretion was two fold, a response equivalent to that observed with 20 mM L-arginine. 5. ICI 118551 significantly inhibited the rise in glucagon secretion induced by clenbuterol (up to 20 microM). 6. The results indicate that the rat islet A cell population is equipped with functional beta 2-adrenoceptors which influence glucagon secretion via the second messenger cyclic AMP, but that the B cells are deficient in functional beta-receptors.
SMART--An Integrated Wireless System for Monitoring Unattended Patients (2007)

Monitoring vital signs and locations of certain classes of ambulatory patients can be useful in overcrowded emergency departments and at disaster scenes, both on-site and during transportation. To be useful, such monitoring needs to be portable and low cost, and have minimal adverse impact on emergency personnel, e.g., by not raising an excessive number of alarms. The SMART (Scalable Medical Alert Response Technology) system integrates wireless patient monitoring (ECG, SpO(2)), geo-positioning, signal processing, targeted alerting, and a wireless interface for caregivers. A prototype implementation of SMART was piloted in the waiting area of an emergency department and evaluated with 145 post-triage patients. System deployment aspects were also evaluated during a small-scale disaster-drill exercise.
Zinc is required for folding and binding of a single zinc finger to DNA (1991)

A synthetic peptide corresponding to zinc finger 31 of the Xenopus protein Xfin adopts a folded conformation in the presence of zinc. The same peptide in the absence of zinc is not folded in a stable tertiary conformation, as determined by NMR. Binding experiments have shown that the peptide binds non-specifically to DNA only in the presence of zinc. Moreover, competitive DNA binding experiments indicate interaction with 3.9 +/- 0.4 base pairs.
Clinical Significance of the Mesenteric Blood Level of CYFRA21-1 in Patients with Colorectal Cancer. Patients at risk for postoperative hematogenous metastasis. (2002)

大腸癌60例(Dukes A:5例,B:28例,C:15例,D:12例)を対象に,還流静脈血中のCYFRA21-1(以下,シフラ)を測定し,同時採取した還流静脈血CEA,病理学的因子および術後再発との関係から,その臨床的意義を検討した.還流静脈血中のシフラはCEAとの問に相関は認められなかったが,病理学的因子では,CEAと同様に壁深達度,リンパ節転移,肝転移,ly因子において有意に高値を示した.また血行性転移の低危険群と高危険群の弁別に微小血管密度,還流静脈血シフラ値,末梢血CEA値を用いて線形判別分析を施行した結果,高値の判別成功率が得られた.さらに大腸癌47例の予後検討では,高危険群4例中3例に血行性再発が認められ,シフラは大腸癌の予後判定のうえで有用なマーカーの一つと考えられた.
P459 Predominant dysbiosis in patients with ulcerative colitis is different from Crohn's disease patients (2012)

P459 Predominant dysbiosis in patients with ulcerative colitis is different from Crohn’s disease patients K. Machiels1 *, M. Joossens1,2,3, J. Sabino1, V. De Preter1, I. Arijs1, V. Ballet1, K. Claes1, J. Verhaegen1, G. Van Assche1, P. Rutgeerts1, S. Vermeire1. 1University Hospital Gasthuisberg, Leuven, Belgium, 2Research group of Bioinformatics and (eco-)systems biology, Department of Structural Biology, VIB, Brussels, Belgium, 3Research group of Bioinformatics and (eco-)systems biology, Microbiology Unit (MICR), Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
Relationship of cell growth to the regulation of tissue‐specific gene expression during osteoblast differentiation (1990)

The relationship of cell proliferation to the temporal expression of genes characterizing a developmental sequence associated with bone cell differentiation can be examined in primary diploid cultures of fetal calvarial-derived osteoblasts by the combination of molecular, biochemical, histochemical, and ultrastructural approaches. Modifications in gene expression define a developmental sequence that has 1) three principal periods: proliferation, extracellular matrix maturation, and mineralization; and 2) two restriction points to which the cells can progress but cannot pass without further signals. The first restriction point is when proliferation is down-regulated and gene expression associated with extracellular matrix maturation is induced, and the second when mineralization occurs. Initially, actively proliferating cells, expressing cell cycle and cell growth regulated genes, produce a fibronectin/type I collagen extracellular matrix. A reciprocal and functionally coupled relationship between the decline in proliferative activity and the subsequent induction of genes associated with matrix maturation and mineralization is supported by 1) a temporal sequence of events in which an enhanced expression of alkaline phosphatase occurs immediately after the proliferative period, and later an increased expression of osteocalcin and osteopontin at the onset of mineralization; 2) increased expression of a specific subset of osteoblast phenotype markers, alkaline phosphatase and osteopontin, when proliferation is inhibited; and 3) enhanced levels of expression of the osteoblast markers when collagen deposition is promoted, suggesting that the extracellular matrix contributes to both the shutdown of proliferation and development of the osteoblast phenotype. The loss of stringent growth control in transformed osteoblasts and in osteosarcoma cells is accompanied by a deregulation of the tightly coupled relationship between proliferation and progressive expression of genes associated with bone cell differentiation.
SuperHirn – a novel tool for high resolution LC‐MS‐based peptide/protein profiling (2007)

Label-free quantification of high mass resolution LC-MS data has emerged as a promising technology for proteome analysis. Computational methods are required for the accurate extraction of peptide signals from LC-MS data and the tracking of these features across the measurements of different samples. We present here an open source software tool, SuperHirn, that comprises a set of modules to process LC-MS data acquired on a high resolution mass spectrometer. The program includes newly developed functionalities to analyze LC-MS data such as feature extraction and quantification, LC-MS similarity analysis, LC-MS alignment of multiple datasets, and intensity normalization. These program routines extract profiles of measured features and comprise tools for clustering and classification analysis of the profiles. SuperHirn was applied in an MS1-based profiling approach to a benchmark LC-MS dataset of complex protein mixtures with defined concentration changes. We show that the program automatically detects profiling trends in an unsupervised manner and is able to associate proteins to their correct theoretical dilution profile.
An Efficient Convergent Synthesis of GP1c Ganglioside Epitope (2008)

In this report, we describe an efficient convergent synthesis of the GP1c glycolipid epitope, which is one of the most complex c-series gangliosides. The alpha(2,3) and alpha(2,8) sialylations were accomplished by use of 5N,4O-carbonyl and 7,8-O-isopropyliden as well as 5N,4O-carbonyl- and 7,8-di-O-chloroacetyl-protected sialyl donors in good yields with excellent alpha-selectivity, respectively. The two sialyl donors enable synthesis of the di- and trisialylgalactosides by simple glycosylation and deprotection. We synthesized the protected GP1c glycolipid epitope, which is a compact, rigid, branched structure, via direct coupling of tetarasaccharide and pentasaccharide units.
Children's and adults' attitudes towards parents smacking their children (1995)

Australian children's interests groups are campaigning for legislation to prohibit adults from using physical punishment with children. In this study, 100 South Australian children, early childhood university students and parents were questioned about their personal experiences of physical punishment in childhood. All three groups had strong negative recollections of being smacked. All of the adult subjects agreed that physical violence is damaging to children's psychological development and they knew that smacking is banned in South Australian state schools and pre-schools. Nevertheless a significant number (79%) used physical punishment for disciplining their own children. Furthermore, 80% of parents and early childhood education students opposed State legislation to ban hand-smacking and only 50% approved legislation to ban adults from hitting children with an implement. Although the university students had been taught and used positive child management techniques in schools and pre-schools, 65% said that they would smack their own children for ‘naughty’ behaviour. The study suggests that early learning (even learning of a negative nature) can take precedence over professionally gained knowledge and professional practice. Advocacy groups would be advised to press for community education encouraging the use of alternative child management techniques before introducing changes to legislation.