gebhart/patrepeval huggingface dataset:
Delayed administration of anti-PD-1 antibody reverses immune dysfunction and improves survival during sepsis (2010)

There is increasing recognition that a major pathophysiologic event in sepsis is the progression to an immunosuppressive state in which the host is unable to eradicate invading pathogens. Although there are likely numerous causes for the immunosuppression, expression of negative costimulatory molecules on immune effector cells is a likely contributing factor. PD-1 is a recently described, negative costimulatory molecule that has potent effects to inhibit T cell activation, cytokine production, and cytotoxic functions. PD-1 plays a critical role in the host response to specific pathogens, but relatively little work has been done on the possible effects of PD-1 in sepsis. We hypothesized that the anti-PD-1 antibody would improve survival in sepsis. Mice underwent CLP, and PD-1 expression was quantitated. Additionally, the effects of anti-PD-1 antibody on lymphocyte apoptosis, cytokine production, host immunity, and survival were determined. PD-1 expression increased beginning 48 h after sepsis, and >20% of CD4 and CD8 T cells were positive by 7 days. Anti-PD-1 antibody administered 24 h after sepsis prevented sepsis-induced depletion of lymphocytes and DCs, increased Bcl-xL, blocked apoptosis, and improved survival. Anti-PD-1 also prevented the loss in DTH, a key indicator of immunocompetence in sepsis. Thus, delayed administration of anti-PD-1 antibody, an important therapeutic advantage, was effective in sepsis. Furthermore, these results add to the growing body of evidence that modulation of the positive and negative costimulatory pathways on immune cells represents a viable therapeutic approach in reversing immunosuppression and improving sepsis survival.
Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays (2003)

Alternative pre-messenger RNA (pre-mRNA) splicing plays important roles in development, physiology, and disease, and more than half of human genes are alternatively spliced. To understand the biological roles and regulation of alternative splicing across different tissues and stages of development, systematic methods are needed. Here, we demonstrate the use of microarrays to monitor splicing at every exon-exon junction in more than 10,000 multi-exon human genes in 52 tissues and cell lines. These genome-wide data provide experimental evidence and tissue distributions for thousands of known and novel alternative splicing events. Adding to previous studies, the results indicate that at least 74% of human multi-exon genes are alternatively spliced.
Synthesis and antitumor activity of fused tetracyclic quinoline derivatives. 1 (1989)

Several fused tri- and tetracyclic quinolines (I and II) with [2-methoxy-4-[(methylsulfonyl)amino]phenyl]amino or [3-(N,N-dimethylamino)propyl]amino side chains were prepared, and their DNA intercalative properties, KB cytotoxicity, antitumor activity (P388 leukemia), and ability to induce topoisomerase II dependent DNA cleavage were investigated. Some compounds having both intercalative ability and KB cytotoxicity were found to be inactive in vivo. However, a positive correlation was seen between the ability to induce topoisomerase II dependent DNA cleavage and antitumor activity in vivo. The indeno- (13a), benzofuro- (21a), and benzothieno- (22a) quinoline derivatives exhibited potent antitumor activities in vitro and in vivo, comparable to those of m-AMSA. They also intercalate DNA and induce topoisomerase II dependent DNA cleavage. Extended screening of 13a showed it to be active against solid tumors such as M5076 sarcoma, B16 melanoma, and colon 38 carcinoma.
Palladium-Catalyzed Cross-Coupling Reactions between Dihydropyranylindium Reagents and Aryl Halides. Synthesis of C-Aryl Glycals (2003)

[reaction: see text] Palladium(0)-catalyzed cross-coupling reactions between tris(dihydropyranyl)indium 1 and aryl halides 2 have been investigated. Aryl iodides and electron-deficient aryl bromides couple efficiently with the in situ-generated indium reagents in the presence of 1-5 mol % Cl(2)Pd(PPh(3))(2) to produce substituted dihydropyrans 3 with minimal (<10%) dimer (4) formation. Organoindium reagents derived from D-glucal also undergo cross couplings with aryl iodides to produce C-aryl glycals.
Loperamide test: a simple and highly specific screening test for hypercortisolism in children and adolescents (1997)

The overnight dexamethasone (DXM) test can give false-positive results in a few conditions (e.g. stress, strenuous exercise, depression, anorexia, anxiety, anticonvulsive therapy) in diagnosing simple obesity and hypercortisolism (HC). The loperamide (LP; a peripheral opioid agonist) test has proven useful in such conditions in adults. Thirty-one obese subjects (age 10.0-19.7 y) were studied by both overnight DXM test and LP test (8 mg orally, samples for cortisol at 0, 90, 150, 180 and 210 min) on 2 separate days. LP suppressed cortisol (< or = 138 nmol l-1) at a dose of 0.1 mg kg-1 bw (half the minimum recommended dose for the drug's antidiarrhoea effect) in 14 subjects who had normal urinary (< 4970 nmol l-1) and serum (< 552 nmol l-1) cortisol, in the absence of signs and symptoms of HC (group A). The DXM test failed to suppress cortisol in three subjects in group A, two of whom were on anticonvulsive treatment. The LP test suppressed cortisol in all of 13 subjects with elevated urinary and/or serum cortisol and/or with signs or symptoms of HC (but in whom HC was subsequently excluded on clinical grounds) (group B), while the DXM test failed to suppress cortisol in three subjects of this group. One of these was under anticonvulsive treatment and one suffered from anxiety and depression. In four patients with Cushing's syndrome (group C) neither DXM nor LP could suppress cortisol levels. Therefore, the sensitivity was 100% for both DXM and LP, while the specificity was 84% for DXM and 100% for LP. No side-effects were observed with either drug. In conclusion, LP is a useful alternative to DXM in those particular conditions that can affect its specificity in children.
Iatrogenic superior vena cava syndrome. A new entity (1984)

Four patients with cancer developed superior vena cava syndrome following placement of a central venous catheter (Broviac or Hickman catheter) without evidence of mediastinal tumoral involvement. Diagnostic and therapeutic considerations are discussed.
Microfluidic device for multimodal characterization of pancreatic islets (2008)

A microfluidic device to perfuse pancreatic islets while simultaneously characterizing their functionality through fluorescence imaging of the mitochondrial membrane potential and intracellular calcium ([Ca(2+)](i)) in addition to enzyme linked immunosorbent assay (ELISA) quantification of secreted insulin was developed and characterized. This multimodal characterization of islet function will facilitate rapid assessment of tissue quality immediately following isolation from donor pancreas and allow more informed transplantation decisions to be made which may improve transplantation outcomes. The microfluidic perfusion chamber allows flow rates of up to 1 mL min(-1), without any noticeable perturbation or shear of islets. This multimodal quantification was done on both mouse and human islets. The ability of this simple microfluidic device to detect subtle variations in islet responses in different functional assays performed in short time-periods demonstrates that the microfluidic perfusion chamber device can be used as a new gold standard to perform comprehensive islet analysis and obtain a more meaningful predictive value for islet functionality prior to transplantation into recipients, which is currently difficult to predict using a single functional assay.
Ultraviolet-mediated antibiotic activity of species of Compositae caused by polyacetylenic compounds. (1978)

A survey of North, Central, and South American composites, and of certain polyacetylenic compounds occurring in them, confirmed that the ultraviolet-mediated antibiotic activity against Candida albicans can be ascribed to the presence of particular polyacetylenes and their thiophene derivatives. Leaves, stems, roots, and achenes were assayed separately. An attempt was made to relate the phototoxic activity of specific compounds to their chemical structures. Most composites tested were not phototoxic against Candida, but many were antibiotic. The antibiotic activity also appears to be caused by polyacetylenes. Of 65 sequiterpene lactones assayed, only a few were found to be antibiotic, and only one, glaucolide G, was phototoxic.
The Evolution of Chronic Migraine: Classification and Nomenclature (2009)

After nearly 3 decades of debate, the headache community still lacks globally accepted criteria for chronic migraine. This review summarizes the evolution of chronic migraine nomenclature and criteria. We concluded that although there are discrepancies in the currently proposed criteria, there is a significant amount of overlap with previously used classifications such that they all appear to describe the same subset of highly burdened migraine patients. In order to continue to understand the natural history of chronic migraine, address the unmet medical need, and develop effective therapies, field experts and physicians must have a classification that is well understood and accepted by the broader clinical community. It is our view that of the currently established classifications, the Silberstein and Lipton revised criteria for transformed migraine are the most applicable to daily clinical practice and field research.
T Helper Cell Fate Specified by Kinase-Mediated Interaction of T-bet with GATA-3 (2005)

Cell lineage specification depends on both gene activation and gene silencing, and in the differentiation of T helper progenitors to Th1 or Th2 effector cells, this requires the action of two opposing transcription factors, T-bet and GATA-3. T-bet is essential for the development of Th1 cells, and GATA-3 performs an equivalent role in Th2 development. We report that T-bet represses Th2 lineage commitment through tyrosine kinase-mediated interaction between the two transcription factors that interferes with the binding of GATA-3 to its target DNA. These results provide a novel function for tyrosine phosphorylation of a transcription factor in specifying alternate fates of a common progenitor cell.
Absolute Beginner's Guide to Networking (1993)

From the Publisher:

Absolute Beginner's Guide to Networking, 3rd Edition will give the reader the ability and understanding necessary to create and administer a network. The reader will be able to physically connect computers and other devices to the network and access peripherals such as printers over the network. They will also be able to configure computers to access the network and configure the network to share an Internet connection.
This book will provide easy to understand details on new technologies and the back-story information (such as basic networking including protocols and physical infrastructure) necessary for the user to network computer devices. 
Absolute Beginner's Guide to Networking, 3rd Edition will take the frustration out of planning and creating a network. It will help the reader understand what they are getting into when planning a network and strategies for making the network an asset and success.
The reader will:
Learn how to build and effectively use a network
Learn how the elements of a network fit together
Understand networking concepts
Healing from War and Trauma: Southeast Asians in the U.S., A Buddhist Perspective and the Harvard Program in Refugee Trauma (2008)

This paper is the written counterpart to a presentation given in Ha Noi, Vietnam, May 15, 2008 during the United Nations Day of Vesak 2008 Convention, on the effects of war and healing. The paper introduces the work of the Harvard Program in Refugee Trauma (HPRT) located in Boston, Massachusetts. It describes the HPRT Global Mission of education and capac- ity building of health care professionals, international relief workers and policy makers in the area of mental health in nations suffering post-conflict and disaster recovery. In particular the paper discusses the HPRT's unique approach to assisting individuals with severe traumatic his- tories as seen through the lens of the author's work as a psychopharmacologist with Southeast Asians and a team member of the HPRT in Lynn, Massachusetts, through the Lynn Community Health Center (LCHC). LCHC is a multi-disciplinary outpatient health service clinic located north of Boston, Massachusetts. Many patients who have survived genocide, torture, imprison- ment, and war suffer from chronic Post Traumatic Stress Disorder (PTSD) with the sequellae of depression, nightmares, inability to work gainfully, and panic anxiety. Two stories of actual patients (their identifying data protected) are presented to illustrate self-healing and the role of mindfulness, the function of memory in storytelling and recovery, and the value of spirituality, work and altruism in healing.
Frequency Modulation and the Effects of a Periodic Capacity Variation in a Nondissipative Oscillatory Circuit (1933)

Certain fundamental characteristics of the theory of frequency modulation for arbitrarily large degrees of modulation and unrestricted modulation frequencies are developed from the differential equation for a dissipationless circuit with fixed inductance and variable capacitance. The several modes of modulating the frequency are discussed and classified; it is shown that they give the same results only when the amount of modulation is very small. The case of "inverse capacity modulation" is then treated in detail. This treatment discloses the possibility of unstable oscillations occurring with certain values of the parameters; the nature and physical significance of these unstable oscillations are determined, and it is explained why they are not ordinarily observable in radio-frequency modulation or in the warble tone generator. The frequency spectrum of the stable oscillations is found, and a means of calculating the amplitude given. For certain adjustments of the circuit the oscillations may be represented by a true Fourier series, while in general this is not the case. Frequency modulation in radiotelephony, the warble tone, and the special case where the natural period of the unmodulated circuit and the frequency of modulation are of comparable magnitude, represent successively more complicated cases of the same general phenomena; the latter is of special interest. The nature of the phenomena accompanying other than a sinusoidal inverse capacity variation is mentioned.
Graph automorphism perception algorithms in computer-enhanced structure elucidation (1993)

The concept of graph symmetry is explained in terms of the vertex automorphism group, which is a subgroup of the complete vertex permutation group. The automorphism group can be deduced from the automorphism partition of graph vertices. An algorithm is described which constructs the automorphism group of a graph from the automorphism vertex partitioning. The algorithm is useful especially for graphs which contain more than one vertex-partition set. Several well-known topological symmetry perception algorithms that yield automorphism partitions are compared. The comparison is favorable to the Shelley-Munk algorithm, developed in the framework of the SESAMI system for computer-enhanced structure elucidation.
SU11248 maintenance therapy prevents tumor regrowth after fractionated irradiation of murine tumor models. (2003)

Receptor tyrosine kinase activation contributes to cell viability during cytotoxic therapy. The novel broad spectrum receptor tyrosine kinase inhibitor, SU11248, inhibits vascular endothelial growth factor receptor 2, platelet-derived growth factor receptor, c-kit, and fetal liver tyrosine kinase 3. In this study, we maintained SU11248 plasma levels beyond the completion of radiotherapy to determine whether tumor regrowth can be delayed. The antiangiogenic effects of SU11248 were demonstrated using human umbilical vein endothelial cells in vitro. Apoptosis increased and clonogenic survival decreased when SU11248 was used in combination with radiation from 0 to 6 Gy on endothelial cells. In vivo tumor growth delay was increased in C57B6J mice with Lewis lung carcinoma or glioblastoma multiform (GL261) hind limb tumors. Mice were treated with daily i.p. injections (40 mg/kg) of SU11248 during 7 days of radiation treatment (21 Gy). Combined treatment with SU11248 and radiation significantly reduced tumor volume as compared with either treatment alone. Concomitant reduction in vasculature was confirmed using the dorsal vascular window model. The vascular length established using images taken from a consistent quadrant in the window show the combination therapy was more effective in destroying tumor vasculature than either treatment alone. SU11248 maintenance administration beyond the completion of radiotherapy results in prolongation of tumor control. In summary, SU11248 enhances radiation-induced endothelial cytotoxicity, resulting in tumor vascular destruction and tumor control when combined with fractionated radiotherapy in murine tumor models. Moreover, inhibition of angiogenesis well beyond radiation therapy may be a promising treatment paradigm for refractory human neoplasms.
Proteolysis in colorectal cancer. (1999)

The increased extracellular proteinase concentrations and activity may encourage tumour invasion and metastasis. This study points to MMP-9 as being of potential major importance in the development of this form of cancer.
Human Milk Glycoconjugates That Inhibit Pathogens (1999)

Breast-fed infants have lower incidence of diarrhea, respiratory disease, and otitis media. The protection by human milk has long been attributed to the presence of secretory IgA. However, human milk contains large numbers and amounts of complex carbohydrates, including glycoproteins, glycolipids, glycosaminoglycans, mucins, and especially oligosaccharides. The oligosaccharides comprise the third most abundant solid constituent of human milk, and contain a myriad of structures. Complex carbohydrate moieties of glycoconjugates and oligosaccharides are synthesized by the many glycosyltransferases in the mammary gland; those with homology to cell surface glycoconjugate pathogen receptors may inhibit pathogen binding, thereby protecting the nursing infant. Several examples are reviewed: A fucosyloligosaccharide inhibits the diarrheagenic effect of stable toxin of Escherichia coli. A different fucosyloligosaccharide inhibits infection by Campylobacter jejuni. Binding of Streptococcus pneumoniae and of enteropathogenic E. coli to their respective receptors is inhibited by human milk oligosaccharides. The 46-kD glycoprotein, lactadherin, inhibits rotavirus binding and infectivity. Low levels of lactadherin in human milk are associated with a higher incidence of symptomatic rotavirus in breast-fed infants. A mannosylated glycopeptide inhibits binding by enterohemorrhagic E. coli. A glycosaminoglycan inhibits binding of gp120 to CD4, the first step in HIV infection. Human milk mucin inhibits binding by S-fimbriated E. coli. The ganglioside, GM1, reduces diarrhea production by cholera toxin and labile toxin of E. coli. The neutral glycosphingolipid, Gb3, binds to Shigatoxin. Thus, many complex carbohydrates of human milk may be novel antipathogenic agents, and the milk glycoconjugates and oligosaccharides may be a major source of protection for breastfeeding infants.
Clinical significance of Gremlin 1 in cervical cancer and its effects on cancer stem cell maintenance (2015)

Gremlin 1 is one of the bone morphogenetic protein (BMP) antagonists and is also related to differentiation in combination with BMPs and is associated with various types of diseases. Gremlin 1 is overexpressed in various types of human cancers and has been reported to play a role in cervical cancer oncogenesis. However, there is no report concerning the relationship between Gremlin 1 and cervical cancer stem cells (CSCs). The objective of the present study was to identify the clinical significance of Gremlin 1 in cervical cancer and its effects on CSC-like properties in vitro. Clinical samples were obtained. Gremlin 1 mRNA expression levels in the cervical cancer tissues were measured by RT-qPCR and assessed for correlation with their clinical prognosis [overall survival (OS), progression-free survival (PFS)] and with other prognostic factors. In vitro, cervical cancer, CaSki cells, exposed to Gremlin 1 (1,000 ng/ml) for 24 h were evaluated for expression of undifferentiated-cell markers (Nanog, Oct3/4, Sox2) by RT-qPCR, the population of ALDH-positive cells by flow cytometry and sphere-forming ability on a ultra-low attachment culture dish. Cervical cancer tissues from 104 patients were collected. A high mRNA expression level of Gremlin 1 was an independent poor prognostic factor of PFS but not of OS. A high mRNA expression level of Gremlin 1 was correlated with bulky (>4 cm) tumors. The Nanog mRNA expression level was significantly increased in the CaSki cells exposed to Gremlin 1 (P=0.0008) but not Oct3/4 and Sox2 mRNA expression levels. The population of ALDH-positive cells in the Gremlin 1-exposed cells was 1.41-fold higher compared with the control (P=0.0184). Sphere-forming ability was increased when 1,000 Gremlin 1-exposed cells were seeded (P=0.0379). In cervical cancer, it is suggested that Gremlin 1 may have a role in clinical recurrence and maintaining CSC-like properties.
Antibody Purification: Ion-Exchange Chromatography (2009)

Ion exchange chromatography techniques are the focus of this chapter and they showcase the power of this method for the purification of proteins and monoclonal antibodies. The technique is powerful and can separate biomolecules that have minor differences in their net charge, e.g., two protein molecules differing by a single charged amino acid. Given the amphoteric character of proteins the pH of the solution is important in the determination of the type of ion exchanger used. Immunoglobulins, although they can be purified by either cation or anion exchange chromatography, are most frequently purified by anion exchange with DEAE resins. The purification of the rabbit IgG fraction from serum using a DEAE column is detailed as well as the purification of IgG from ascitic fluid using FPLC, from loading to elution of the purified and concentrated protein.
Serum, salivary and tissue proteomics for discovery of biomarkers for head and neck cancers (2005)

Initial clinically oriented applications of emerging proteomic technologies that aim to identify biomarkers for head and neck squamous cell carcinoma diagnostics have yielded promising results. The development of new proteomic diagnostics remains critical for the early detection of head and neck squamous cell carcinoma at more treatable stages. Prognostic markers for disease recurrence and treatment sensitivities are also required. In this overview of current biomarker identification strategies for head and neck squamous cell carcinoma, different combinations of mass spectrometry platforms, laser capture microscopy and 2D gel electrophoresis procedures are summarized as applied to readily available clinical specimens (tissue, blood and saliva). Issues related to assay reproducibility, management of large data sets and future improvements in clinical proteomics are also addressed.
Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability (2001)

Fluorination of the hydrophobic core of a coiled-coil protein significantly improved its stability toward thermal and chemical denaturation. 5',5',5'-Trifluoroleucine (2) was efficiently incorporated into a leucine-zipper protein in place of leucine (1) during E. coli biosynthesis. The fluorinated variant maintained stable secondary and tertiary structures under conditions that caused denaturation of the "wild-type" protein.