gebhart/patrepeval huggingface dataset:
Activation of human B lymphocytes through CD40 and interleukin 4 (1989)

We have produced and characterized a new CD40 monoclonal antibody, mAb 89, which in the presence of anti-IgM antibodies co-stimulates to induce B cell proliferation. mAb 89 activates resting B cells as shown by an increase in cell volume and an enhanced subsequent proliferation of B cells in response to anti-IgM antibody. However, mAb 89 does not prepare B cells to respond to the growth-promoting activity of interleukin (IL) 2 or IL 4. Unlike IL 2 and IL 4, mAb 89 only weakly stimulates the proliferation of anti-IgM pre-activated B cells. Thus, the activating properties of anti-CD40 are likely to explain its co-stimulatory effect on B cells. Interestingly, the anti-CD40 mAb 89 was found to act in synergy with IL 4, but not with IL 2, in co-stimulation and restimulation assays. In this respect, anti-CD40 does not induce a significant increase of B cell surface IL 4 receptors while IL 4, but not IL 2, induces a twofold increase of the CD40 antigen expression. Thus the synergistic interaction between IL 4 and anti-CD40 may be related to the IL 4-dependent increase of CD40 antigen expression.
Camptothecin and Its Analogs (1996)

From the outset of their clinical testing the camptothecins have shown antitumor activity against gastrointestinal cancer. With the definition of mechanism of action and introduction of several analogs their antitumor activity spectrum has expanded to include ovarian, cervical, small-cell and non-small cell lung cancers and malignant lymphomas, among others. The wide range of trials in these disease areas have been reviewed for CPT-11, topotecan, and 9-aminocamptothecin. A therapeutic role is anticipated for these and other camptothecins in these disease sites. Issues in guiding treatment indications and clinical development include: 1) pharmacokinetics and scheduling relevant to each of the drugs, with the oral route emerging as a practical way for testing prolonged exposure; 2) dose-intensification with cytokines, and its relevance in maintaining effective doses particularly in combination with other myelosuppressive drugs; and 3) pharmacodynamic determinants of response-an area of research that is particularly attractive because topoisomerase I is the target for camptothecins.
Short Activated Partial Thromboplastin Times Are Related to Increased Thrombin Generation and an Increased Risk for Thromboembolism (2000)

This prospective study was designed to investigate whether patients with short activated partial thromboplastin times (aPTTs) have increased thrombin generation and are at increased risk for thromboembolism. During a 4-month period, routine coagulation specimens were screened for the presence of a short or normal aPTT, and, accordingly, 250 specimens were collected. Prothrombin fragment F1+2 (F1+2) was measured to evaluate thrombin activation, and a second aPTT was performed with a different reagent. Diagnoses were obtained from medical records after conclusion of sample collection. Five to 9 months later, patients were questioned on thromboembolic events during the previous 18 months by questionnaire and telephone interview. F1+2 and the incidence of venous thromboses were elevated significantly in the short aPTT group. Unexpectedly, patients with acute bleeding had short aPTTs, but 36% of these also had thromboembolic events during the 18 months proximal to blood collection. These findings were confirmed with the second aPTT reagent. Patients with short aPTTs have increased thrombin generation and are at increased risk for thromboembolism, mainly venous thromboses, despite the fact that a short aPTT can occur in the acute setting of bleeding.
Color Gamut Scalable Video Coding (2013)

This paper describes a scalable extension of the High Efficiency Video Coding (HEVC) standard that supports different color gamuts in an enhancement and base layer. Here, the emphasis is on scenarios with BT.2020 color gamut in an enhancement layer and BT.709 color gamut in the base layer. This is motivated by a need to provide content for both high definition and ultra-high definition devices in the near future. The paper describes a method for predicting the enhancement layer samples from a decoded base layer using a series of multiplies and adds to account for both color gamut and bit-depth changes. Results show an improvement in coding efficiency between 65% and 84% for luma (57% and 85% for chroma) compared to simulcast in quality (SNR) scalable coding.
Serum interleukin-2 and tumor necrosis factor-alpha in primary biliary cirrhosis: decrease by colchicine and relationship to HLA-DR4. (1992)

Colchicine improves liver function tests and survival in primary biliary cirrhosis (PBC); however, its mechanism of action in PBC is unknown. Because elevated interleukin-2 (IL-2) and tumor necrosis factor-alpha (TNF) have been found in various inflammatory diseases, we measured serum levels of IL-2 and TNF in 28 PBC patients before and during treatment with either colchicine or placebo. Compared with normal controls, untreated PBC patients had increased serum IL-2 (39 +/- 13 U/ml vs. 0.8 +/- 0.5) and TNF (549 +/- 162 pg/ml vs. nondetectable). During colchicine treatment, both IL-2 and TNF levels decreased significantly (57 +/- 24 to 40 +/- 22, p less than 0.04; 586 +/- 295 to 445 +/- 295, p less than 0.02). No significant changes in IL-2 or TNF levels occurred in the placebo-treated patients. DR4-positive patients had elevated levels of IL-2 at entry, compared with DR4-negative patients (67 +/- 26 vs. 14 +/- 5, p less than 0.04). The effect of colchicine in PBC may be due, in part, to modulation of IL-2 and TNF levels. Alternatively, the changes in IL-2 and TNF may simply reflect the overall improvement in biochemical tests of liver function related to colchicine therapy. DR4 appears to relate to serum levels of these cytokines in PBC and, possibly, also to the response to colchicine.
Dendritic Cell Vaccination Combined with CTLA4 Blockade in Patients with Metastatic Melanoma (2009)

The combination of MART-1 peptide-pulsed DC and tremelimumab results in objective and durable tumor responses at the higher range of the expected response rate with either agent alone.
Expression and Purification of Enzymatically Active Forms of the Human Lysyl Oxidase-like Protein 4 (2003)

The lysyl oxidase-like protein 4 (LOXL4) is the latest member of the emerging family of lysyl oxidases, several of which were shown to function as copper-dependent amine oxidases catalyzing lysine-derived cross-links in extracellular matrix proteins. LOXL4 contains four scavenger receptor cysteine-rich domains in addition to the characteristic domains of the LOX family, including the copper-binding domain, the cytokine receptor-like domain, and the residues of the lysyl-tyrosyl quinone cofactor. In an effort to assess its amine oxidase activity, we expressed LOXL4 as recombinant forms attached with hexa-histidine residues at the carboxyl terminus by using an Escherichia coli expression system. The recombinant proteins were purified with nickel-chelating affinity chromatography and converted into enzymatically active forms by stepwise dialysis. The purified LOXL4 proteins showed beta-aminopropionitrile-inhibitable activity of 0.022-0.032 units/mg toward a nonpeptidyl substrate, benzylamine. These results indicate that LOXL4, with the four scavenger receptor cysteine rich domains, may also function as an active amine oxidase. Availability of the pure and active forms of LOXL4 will be significantly helpful in functional studies related to substrate specificity and crystal structure of this amine oxidase, which should provide significant insights into functional differences within the LOX family members.
Functional tuning of nucleic acids by chemical modifications: Tailored oligonucleotides as drugs, devices, and diagnostics (2003)

Chemical modifications of nucleic acids present vast opportunities for extending the functions and properties of these biomolecules. In general, efforts invested in this direction pertain to the introduction of reactive functional groups for further derivatizations of oligonucleotides with numerous reporter groups and for equipping nucleic acids with catalytic chemical moieties. This review deals with representative chemical modifications in the nucleobases, sugars, and the phosphate ester backbone and their application from novel catalytic RNA selection to nucleic acid-based biosensors.
A Pathogenic Retrovirus (HTLV-III) Linked to AIDS (1984)

APPROXIMATELY three years ago an apparently new and unexplained disorder called the acquired immunodeficiency syndrome (AIDS) was recognized. Prompt worldwide recognition of this syndrome was brought about by a truly remarkable collaboration between practicing physicians in several parts of the United States and epidemiologists at the Centers for Disease Control. AIDS immediately became the subject of a number of reports, many of which have appeared in the Journal.1 2 3 4 5 6 7 8 9 The disorder is an epidemic immunosuppressive disease that predisposes to life-threatening infections with opportunistic organisms, Kaposi's sarcoma, and less commonly, other neoplasms such as non-Hodgkin's lymphomas. Characteristically, AIDS is associated with . . .
Oxalate oxidases and differentiating surface structure in wheat: germins (2000)

Oxalate oxidases (OXOs) have been found to be concentrated in the surface tissues of wheat embryos and grains: germin is concentrated in root and leaf sheaths that surround germinated embryos; pseudogermin (OXO-ψ) is concentrated in the epidermis and bracts that ‘encircle’ mature grains. Most strikingly, the epidermal accumulation of OXO-ψ was found to presage the transition of a delicate ‘skin’, similar to the fragile epidermis of human skin, into the tough shell (the miller's ‘beeswing’) that is typical of mature wheat grains. A narrow range of oxalate concentration (1-2 mM) in the hydrated tissues of major crop cereals (barley, maize, oat, rice, rye and wheat) contrasted with wide variations in their OXO expression, e.g. cold-tolerant and cold-sensitive varieties of maize have similar oxalate contents but the former was found to contain approx. 20-fold more germin than did the latter. Well-known OXOs in sorghum, a minor cereal, and beet, a dicotyledon, were found to have little antigenic relatedness to the germins, but the beet enzyme did share some of the unique stability properties that are peculiar to the germin-like OXOs that are found only in the major crop cereals. Their concentration in surface structures of domesticated wheat suggests a biochemical role for germin-like OXOs: programmed cell death in surface tissues might be a constitutive as well as an adaptive form of differentiation that helps to produce refractory barriers against tissue invasion by predators. Incidental to the principal investigation, and using an OXO assay (oxalate-dependent release of CO2) that did not rely on detecting H2O2, which is often fully degraded in cell extracts, it was found that OXO activity in soluble extracts of wheat was manifested only in standard solution assays if the extract was pretreated in a variety of ways, which included preincubation with pepsin or highly substituted glucuronogalactoarabinoxylans (cell-wall polysaccharides).
beta-Amyloid-induced neuronal apoptosis requires c-Jun N-terminal kinase activation (2001)

beta-Amyloid (A beta) has been strongly implicated in the pathophysiology of Alzheimer's disease (AD), but the means by which the aggregated form of this molecule induces neuronal death have not been fully defined. Here, we examine the role of the c-Jun N-terminal kinases (JNKs) and of their substrate, c-Jun, in the death of cultured neuronal PC12 cells and sympathetic neurons evoked by exposure to aggregated A beta. The activities of JNK family members increased in neuronal PC12 cells within 2 h of A beta treatment and reached 3--4-fold elevation by 6 h. To test the role of these changes in death caused by A beta, we examined the effects of CEP-1347 (KT7515), an indolocarbazole that selectively blocks JNK activation. Inclusion of CEP-1347 (100--300 nM) in the culture medium effectively blocked the increases in cellular JNK activity caused by A beta and, at similar concentrations, protected both PC12 cells and sympathetic neurons from A beta-evoked-death. Effective protection required addition of CEP-1347 within 2 h of A beta treatment, indicating that the JNK pathway acts relatively proximally and as a trigger in the death mechanism. A dominant-negative c-Jun construct also conferred protection from A beta-evoked death, supporting a model in which JNK activation contributes to death via activation of c-Jun. Finally, CEP-1347 blocked A beta-stimulated activation of caspase-2 and -3, placing these downstream of JNK activation. These observations implicate the JNK pathway as a required element in death evoked by A beta and hence identify it as a potential therapeutic target in AD.
Oral tolerance in the absence of naturally occurring Tregs (2005)

Mucosal tolerance prevents pathological reactions against environmental and food antigens, and its failure results in exacerbated inflammation typical of allergies and asthma. One of the proposed mechanisms of oral tolerance is the induction of Tregs. Using a mouse model of hyper-IgE and asthma, we found that oral tolerance could be effectively induced in the absence of naturally occurring thymus-derived Tregs. Oral antigen administration prior to i.p. immunization prevented effector/memory Th2 cell development, germinal center formation, class switching to IgE, and lung inflammation. Oral exposure to antigen induced development of antigen-specific CD4CD25Foxp3CD45RB cells that were anergic and displayed suppressive activity in vivo and in vitro. Oral tolerance to the Th2 allergic response was in large part dependent on TGF-beta and independent of IL-10. Interestingly, Tregs were also induced by single i.p. immunization with antigen and adjuvant. However, unlike oral administration of antigen, which induced Tregs but not effector T cells, i.p. immunization led to the simultaneous induction of Tregs and effector Th2 cells displaying the same antigen specificity.
Role of Rhizobium endoglucanase CelC2 in cellulose biosynthesis and biofilm formation on plant roots and abiotic surfaces (2012)

Our results support a key role of the CelC2 cellulase in cellulose biosynthesis by modulating the length of the cellulose fibrils that mediate firm adhesion among Rhizobium bacteria leading to biofilm formation. Rhizobium cellulose is an essential component of the biofilm polysaccharidic matrix architecture and either an excess or a defect of this "building material" seem to collapse the biofilm structure. These results position cellulose hydrolytic enzymes as excellent anti-biofilm candidates.
A Generalizing Adaptive Discriminant Network (1993)

This study aims to investigate the relationship between single nucleotide polymorphisms (SNPs) of sex hormone binding globulin (SHBG) and type 2 diabetes mellitus (T2DM) in an Uighur population. One hundred and fourteen T2DM male patients (with a history of diabetes or diagnosed as diabetic by the oral glucose tolerance test) and 173 healthy males from the Uighur ethnic group were included in the study to test the following SNPs of SHBG: rs727428, rs1799941, rs6259, rs6257, rs858521, rs858518, rs3760213, and rs11078701. The body mass index (BMI), blood pressure, and waist circumference, and lipid, glucose, HbA1c, insulin, HOMA-IR, testosterone, and SHBG levels of enrolled individuals were measured. We used the t-test or rank sum test and Chi-square test to analyze the difference and compare numeration data, respectively, between the case and control groups. Comparisons among multiple groups were carried out using analysis of variance, and the correlation between variables was determined by nonparametric Spearman rank correlation analysis; multivariate logistic regression analysis was used to assess the risk of abnormal glucose in the two groups. There was a significant difference (<i>P</i> < 0.05) in BMI, blood pressure, and waist circumference, and lipid, glucose, HbA1c, insulin, and HOMA-IR levels between the case and control groups. The risk factors for diabetes included testosterone (<i>P</i> = 0.042) and SHBG (<i>P</i> = 0.001). The distribution of rs858521 (<i>P</i> = 0.001), rs1799941 (2.3%, <i>P</i> = 0.032), rs6259 (2.5%, <i>P</i> = 0.040), and rs727428 (3.4%, <i>P</i> = 0.016) was significantly different between the case and control groups (<i>P</i> < 0.05). In the control group, there was linkage disequilibrium (LD) between rs727428 and rs6259, while in the case group LD was found among rs858518, rs3760213, rs1799941, and rs6257. The frequency of rs858518-rs3760213-rs1799941-rs6257 haplotype TCGC was significantly different between the two groups (<i>P</i> = 0.033). Both testosterone and SHBGwere found to be risk factors of diabetes in the Uighur population, and SNPs of SHBG may contribute to T2DM.
Moviescope: Large-scale Analysis of Movies using Multiple Modalities (2019)

Film media is a rich form of artistic expression. Unlike photography, and short videos, movies contain a storyline that is deliberately complex and intricate in order to engage its audience. In this paper we present a large scale study comparing the effectiveness of visual, audio, text, and metadata-based features for predicting high-level information about movies such as their genre or estimated budget. We demonstrate the usefulness of content-based methods in this domain in contrast to human-based and metadata-based predictions in the era of deep learning. Additionally, we provide a comprehensive study of temporal feature aggregation methods for representing video and text and find that simple pooling operations are effective in this domain. We also show to what extent different modalities are complementary to each other. To this end, we also introduce Moviescope, a new large-scale dataset of 5,000 movies with corresponding movie trailers (video + audio), movie posters (images), movie plots (text), and metadata.
Copper‐Catalyzed Double Additions and Radical Cyclization Cascades in the Re‐Engineering of the Antibacterial Pleuromutilin (2015)

A general synthetic sequence involving simply prepared starting materials provides rapid access to diverse, novel tricyclic architectures inspired by pleuromutilin. Sm(II) -mediated radical cyclization cascades of dialdehydes, prepared using a new, one-pot, copper-catalyzed double organomagnesium addition to β-chlorocyclohexenone, proceed with complete sequence selectivity and typically with high diastereocontrol to give analogues of the target core. Our expedient approach (ca. 7 steps) allows non-traditional, de novo synthetic access to analogues of the important antibacterial that can't be prepared from the natural product by semisynthesis.
FolM, A New Chromosomally Encoded Dihydrofolate Reductase in Escherichia coli (2003)

Escherichia coli (thyA DeltafolA) mutants are viable and can grow in minimal medium when supplemented with thymidine alone. Here we present evidence from in vivo and in vitro studies that the ydgB gene determines an alternative dihydrofolate reductase that is related to the trypanosomatid pteridine reductases. We propose to rename this gene folM.
Fine Needle Aspiration Cytology of Metastatic Nasopharyngeal Undifferentiated Carcinoma of Lymph Node - Report of a Case Presenting Spindle Cell Pattern - (1993)

We describe a case of fine needle aspiration cytology of metastatic nasopharyngeal carcinoma in the lymph node of the neck presenting a predominantly spindle cell pattern. A 36 year-old male patient complained of dysesthesia on the right face and a palpable neck mass. Fine needle aspiration was done on the neck mass. Tumor cells were present in syncytial groups or singly with mainly spindle shaped nuclei, vesicular chromatin, thin and regular nuclear membrane, occasional prominent nucleoli and a few fool of cellular cohesiveness. The cytoplasm was scant and pale with ill-defined borders. Mature lymphocytes were present in the background of aspirates and within the tumor cell clusters. Histologically, the tumor of nasopharynx showed several areas of spindle cell pattern. Because the tumor cells showed a predominantly spindle shape with vesicular nuclear chromatin, the differential diagnosis of spindle cell sarcoma or granuloma of epithelioid clils were considered, but the characteristic morphology of the nuclei with vesicular chromatin and prominent nucleoli, and cellular cohesiveness were important in making the diagnosis of nasopharyngeal carcinoma. The possibility of metastatic carcinoma should always be considered in fine needle aspiration cytology of the lymph node in the neck because the incidence of metastatic carcinoma, particularly of the nasopharyngeal carcinoma in the lymph nodes of the neck is relatively high.
Levels of soluble ST2 in serum associated with severity of dengue due to tumour necrosis factor alpha stimulation (2009)

The interleukin-1 receptor-like-1 protein (IL1RL1), also known as ST2, has been shown previously to regulate T-cell function and is produced by T cells and endothelial cells. It was reported recently to be elevated in mild dengue patients during acute disease. The ST2 gene encodes several splice products: L (long), V (short) and s (soluble). A cohort of 38 patients with dengue haemorrhagic fever (DHF) and mild dengue fever (DF) were evaluated using a secreted soluble ST2 (sST2) ELISA. The RNA expression of ST2 was evaluated by real-time quantitative RT-PCR using patients' peripheral blood mononuclear cells (PBMCs) and in vitro using human umbilical vein endothelial cells (HUVECs) exposed to sera from dengue patients. DHF patients had higher levels of serum sST2, tumour necrosis factor alpha (TNF-alpha), interleukin (IL)-8 and IL-10 compared with DF patients and normal healthy control individuals. However, viraemia was indistinguishable between mild and severe cases. No changes in ST2 mRNA expression were found in PBMCs from these two groups of dengue patients. In vitro, sST2 was elevated in HUVECs treated with patient sera. Neutralization of TNF-alpha in patient sera by pre-treatment with a TNF-alpha antibody inhibited the upregulation of sST2 expression in HUVECs. These results implicate serum TNF-alpha in the modulation of expression of sST2 in an in vitro system, and indicate that sST2 could be associated with the severity of disease. Further studies to determine whether sST2 levels are predictive of the severe form of the disease and the role of sST2 in immune regulation are warranted.
The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces (2012)

Vibrio cholerae is a bacterial pathogen that colonizes the chitinous exoskeleton of zooplankton as well as the human gastrointestinal tract. Colonization of these different niches involves an N-acetylglucosamine binding protein (GbpA) that has been reported to mediate bacterial attachment to both marine chitin and mammalian intestinal mucin through an unknown molecular mechanism. We report structural studies that reveal that GbpA possesses an unusual, elongated, four-domain structure, with domains 1 and 4 showing structural homology to chitin binding domains. A glycan screen revealed that GbpA binds to GlcNAc oligosaccharides. Structure-guided GbpA truncation mutants show that domains 1 and 4 of GbpA interact with chitin in vitro, whereas in vivo complementation studies reveal that domain 1 is also crucial for mucin binding and intestinal colonization. Bacterial binding studies show that domains 2 and 3 bind to the V. cholerae surface. Finally, mouse virulence assays show that only the first three domains of GbpA are required for colonization. These results explain how GbpA provides structural/functional modular interactions between V. cholerae, intestinal epithelium and chitinous exoskeletons.
Elagolix Suppresses Ovulation in a Dose-Dependent Manner: Results From a 3-Month, Randomized Study in Ovulatory Women (2019)

Women being treated with elagolix may ovulate and should use effective methods of contraception. The rate of ovulation was lowest with elagolix 300 mg BID plus E2/NETA 1/0.5 mg QD.