gebhart/patrepeval huggingface dataset:
Variation in MHC Expression Between Undifferentiated Mouse ES Cells and ES Cell-derived Insulin-producing Cell Clusters (2009)

These data highlight differences in MHC expression between ES cells and a fully differentiated ES cell derived tissue and suggest how the progeny of ES cells may be susceptible to rejection after transplantation.
Macro-Prudential Policy: An Assessment (2010)

The financial crisis of the past three years has been the most severe episode of global financial instabili-ty since the 1930s. It has resulted in a marked de-cline of world trade, and the first global aggregate
T-bet-dependent expression of osteopontin contributes to T cell polarization (2005)

The osteopontin (Opn) glycoprotein has been implicated in diverse physiological processes, including vascularization, bone formation, and inflammatory responses. Studies of its role in immune responses has suggested that Opn can set the early stage of type-1 immune (cell-mediated) responses through differential regulation of IL-12 and IL-10 cytokine gene expression in macrophages. Although Opn has been suggested to play a role in the development of type-1 immunity, little is known about control of Opn gene expression. Here, we report that Opn gene expression in activated T cells, but not macrophages, is regulated by T-bet, a transcription factor that controls CD4+ T helper (Th1) cell lineage commitment. We also find that T-bet-dependent expression of Opn in T cells is essential for efficient skewing of CD4+ T and CD8+ T cells toward the Th1 and type 1 CD8+ T cells (Tc1) pathway, respectively. Taken together, these findings begin to delineate the genetic basis of Opn expression in T cells and further clarify the role of Opn in Th and Tc1 development.
VISTA, a novel mouse Ig superfamily ligand that negatively regulates T cell responses (2011)

The immunoglobulin (Ig) superfamily consists of many critical immune regulators, including the B7 family ligands and receptors. In this study, we identify a novel and structurally distinct Ig superfamily inhibitory ligand, whose extracellular domain bears homology to the B7 family ligand PD-L1. This molecule is designated V-domain Ig suppressor of T cell activation (VISTA). VISTA is primarily expressed on hematopoietic cells, and VISTA expression is highly regulated on myeloid antigen-presenting cells (APCs) and T cells. A soluble VISTA-Ig fusion protein or VISTA expression on APCs inhibits T cell proliferation and cytokine production in vitro. A VISTA-specific monoclonal antibody interferes with VISTA-induced suppression of T cell responses by VISTA-expressing APCs in vitro. Furthermore, anti-VISTA treatment exacerbates the development of the T cell-mediated autoimmune disease experimental autoimmune encephalomyelitis in mice. Finally, VISTA overexpression on tumor cells interferes with protective antitumor immunity in vivo in mice. These findings show that VISTA, a novel immunoregulatory molecule, has functional activities that are nonredundant with other Ig superfamily members and may play a role in the development of autoimmunity and immune surveillance in cancer.
The study of the reaction of terminated oligomerization in the synthesis of oligo-(β1-6)-glucosamines (2006)

The applicability of terminated oligomerization to the synthesis of oligo-(beta1-6)-glycosamines, fragments of the intercellular polysaccharide adhesin of staphylococci, was studied. The reactions of terminated oligomerization were carried out with mono-, di-, and trisaccharide monomers and N-protected aminopropanol; and spacered mono- and disaccharides as terminating molecules were also attempted. The primary formation of cyclic products of monomer intramolecular glycosylation was observed in almost all the reactions. Only the experiments with the monomer based on the disaccharide bromide under the conditions of the Helferich reaction led to reduced yields (30%) of the cyclic products. However, even in this case, the desired terminated oligosaccharides were generated in approximately 10% yield and mainly were the products of single glycosylation of the terminator by the monomer. These experiments allow the conclusion that, under the examined conditions, the reaction of terminated oligomerization could not result in the synthesis of oligoglucosamines with a high molecular mass.
Role of Substratum Stiffness in Modulating Genes Associated with Extracellular Matrix and Mechanotransducers YAP and TAZ (2012)

The expression of YAP/TAZ and ECM-related-genes is impacted on physiologically relevant substrates. YAP was upregulated in cells on softer substrates. Stiffer substrates resulted in upregulation of canonical Wnt modulators, TAZ and sFRP-1, and thus may influence the progression of glaucoma. These results demonstrate the importance of YAP/TAZ in the HTM and suggest their role in glaucoma.
New charge balancing method based on imbalanced biphasic current pulses for functional electrical stimulation (2012)

A new active charge balancing technique for functional electrical stimulation is presented. This method is adopted in a micro-stimulator to be used in deep brain stimulation application. Simulations in a high-voltage 0.18-μm CMOS technology validates the feasibility of the approach and its low power consumption. The power consumption of the charge-balancing circuits contributes 3.4 % of the overall power consumption of the system.
Electrical inhibition of pain by stimulation of the dorsal columns: preliminary clinical report. (1990)

Electrical Inhibition of Pain by Stimulation of the Dorsal Columns: Preliminary Clinical Report C. SHEALY;J. MORTIMER;JAMES RESWICK; Anesthesia & Analgesia
Resolution requirements and the Johnson criteria revisited (2003)

Since the 1950s, numerous studies have been performed within the surveillance and reconnaissance (S&R) and target acquisition (TA) communities in an attempt to predict information extraction performance as a function of image collection and quality parameters. In general, the work followed two separate paths. The TA community developed models to predict probabilities of detection, recognition, and identification as a function of target size, range, and collection system design/performance parameters (e.g., MRT, FLIR92,NVTHERM,MRC). The S&R community developed models to predict National Imagery Interpretability Ratings (NIIRS) as a function of system design and collection parameters (e.g. IR GIQE). More recently, efforts have linked the two approaches such that NIIRS can be predicted from TA models and probabilities of identification can be predicted from NIIRS. With both approaches, resolution is a dominant term. A considerable amount of variability and uncertainty results from target differences. The criteria used to define the NIIRS generalize target type, size, and level of identification specificity. The TA predictions use the Johnson recognition criteria to relate lines on the target to recognition performance. A recent paper found that TA predictions differed substantially between the visible and IR. Further, the paper reported substantial differences among vehicles in terms of a confusion matrix. This finding was not surprising in light of other research, but suggested the need for a more detailed examination and explanation of results. Accordingly, the current effort was undertaken. Data from a variety of past studies dealing with target recognition were examined relative to the Johnson criteria, along with a more detailed analysis of data from two recent TA studies. A hypothesis of target recognition performance was generated and partially validated using available data.
Risk classification as the basis for clinical staging of diffuse large- cell lymphoma derived from 10-year survival data (1989)

Two hundred and fifty previously untreated adult patients with diffuse large-cell lymphomas were treated with a chemotherapy combination of cyclophosphamide, adriamycin, vincristine, prednisone, and low-dose bleomycin (CHOP-Bleo) with or without radiotherapy between 1974 and 1984. The 10-year survival rates for patients with Ann Arbor stages II, III, or IV disease of 55%, 42%, and 40%, respectively, were not significantly different. However, the survival rate of 76% for patients with stage I disease was clearly better. Factors more indicative of prognosis than stage, as found by univariant analysis, were tumor burden, serum lactic dehydrogenase level (LDH), age, and constitutional symptoms. From these, a multivariant analysis selected tumor burden, LDH level, and age as major independent factors for predicting survival (P less than .001). A prognostic risk model constructed on the basis of tumor burden and LDH levels identified four distinct risk groups (A, B, C, D) with 10-year survival rates of 85%, 66%, and 43% for A, B, and C. No patient in group D survived 10 years. These risk groups also had a strong correlation with complete remission rates and with relapse rates. Thus this model proved more effective for identifying patient populations according to their expected responses, durations of remission, and survivals than the Ann Arbor staging system. Detailed information supporting the use of this system for predicting prognosis and for treatment selection for patients with diffuse large-cell lymphomas is provided.
A Novel Base Promoted Reaction of Methyl 2-Isoxazoline-5-acetates to 5-(2-oxoethyl)-3-isoxazolidinones (1998)

Abstract The 5-(2-aryl-2-oxoethyl)-3-isoxazolidinones 3a-e were prepared from the methyl 3-aryl-2-isoxazoline-5-acetates 2a-e and sodium hexanolate in boiling hexanol in yields from 46 to 86 %. The reaction conditions were optimized and a mechanism for this reaction is proposed and discussed.
Monolithic integration of room-temperature cw GaAs/AlGaAs lasers on Si substrates via relaxed graded GeSi buffer layers (2002)

GaAs/Al x Ga (1−x) As quantum well lasers have been demonstrated via organometallic chemical vapor deposition on relaxed graded Ge/GexSi(1−x) virtual substrates on Si. A number of GaAs/Ge/Si integration issues including Ge autodoping behavior in GaAs, reduced critical thickness due to thermal expansion mismatch, and complications with mirror facet cleaving have been overcome. Despite unoptimized laser structures with high series resistance and large threshold current densities, surface threading dislocation densities for GaAs/AlGaAs lasers on Si substrates as low as 2×106 cm−2 permitted continuous room-temperature lasing at a wavelength of 858 nm. The laser structures are uncoated edge-emitting broad-area devices with differential quantum efficiencies of 0.24 and threshold current densities of 577 A/cm2. Identical devices grown on commercial GaAs substrates showed similar behavior. This comparative data agrees with previous measurements of near-bulk minority carrier lifetimes in GaAs grown on Ge/GeSi/Si substrates.
Human Papillomavirus and Cervical Cancer (2003)

Of the many types of human papillomavirus (HPV), more than 30 infect the genital tract. The association between certain oncogenic (high-risk) strains of HPV and cervical cancer is well established. Although HPV is essential to the transformation of cervical epithelial cells, it is not sufficient, and a variety of cofactors and molecular events influence whether cervical cancer will develop. Early detection and treatment of precancerous lesions can prevent progression to cervical cancer. Identification of precancerous lesions has been primarily by cytologic screening of cervical cells. Cellular abnormalities, however, may be missed or may not be sufficiently distinct, and a portion of patients with borderline or mildly dyskaryotic cytomorphology will have higher-grade disease identified by subsequent colposcopy and biopsy. Sensitive and specific molecular techniques that detect HPV DNA and distinguish high-risk HPV types from low-risk HPV types have been introduced as an adjunct to cytology. Earlier detection of high-risk HPV types may improve triage, treatment, and follow-up in infected patients. Currently, the clearest role for HPV DNA testing is to improve diagnostic accuracy and limit unnecessary colposcopy in patients with borderline or mildly abnormal cytologic test results.
A Bipartite Substrate Recognition Motif for Cyclin-dependent Kinases (2001)

Cy or RXL motifs have been previously shown to be cyclin binding motifs found in a wide range of cyclin-Cdk interacting proteins. We report the first kinetic analysis of the contribution of a Cy motif on a substrate to phosphorylation by cyclin-dependent kinases. For both cyclin A-Cdk2 and cyclin E-Cdk2 enzymes, the presence of a Cy motif decreased the K(m(peptide)) 75-120-fold while the k(cat) remained unchanged. The large effect of the Cy motif on the K(m(peptide)) suggests that the Cy motif and (S/T)PX(K/R) together constitute a bipartite substrate recognition sequence for cyclin-dependent kinases. Systematic changes in the length of the linker between the Cy motif and the phosphoacceptor serine suggest that both sites are engaged simultaneously to the cyclin and the Cdk, respectively, and eliminate a "bind and release" mechanism to increase the local concentration of the substrate. PS100, a peptide containing a Cy motif, acts as a competitive inhibitor of cyclin-Cdk complexes with a 15-fold lower K(i) for cyclin E-Cdk2 than for cyclin A-Cdk2. These results provide kinetic proof that a Cy motif located a minimal distance from the SPXK is essential for optimal phosphorylation by Cdks and suggest that small chemicals that mimic the Cy motif would be specific inhibitors of substrate recognition by cyclin-dependent kinases.
Optimal Universal Quantum Cloning and State Estimation (1998)

We derive a tight upper bound for the fidelity of a universal $N\ensuremath{\rightarrow}M$ qubit cloner, valid for any $M\ensuremath{\ge}N$, where the output of the cloner is required to be supported on the symmetric subspace. Our proof is based on the concatenation of two cloners and the connection between quantum cloning and quantum state estimation. We generalize the operation of a quantum cloner to mixed and/or entangled input qubits described by a density matrix supported on the symmetric subspace of the constituent qubits. We also extend the validity of optimal state estimation methods to inputs of this kind.
Purification and properties of a monoacylglycerol lipase in human erythrocytes (1995)

A membrane-bound monoacylglycerol lipase (MAGL) activity, previously demonstrated in intact human erythrocytes [Boyer, Somma, Vérine, L'Hôte, Finidori, Merger and Arnaud (1981) J. Clin. Endocrinol. Metab. 53, 143-148], has now been purified to apparent homogeneity by a five-step procedure involving solubilization in CHAPS and sequential chromatographies on Sephacryl S-400, DEAE-Trisacryl, Zn(2+)-chelating Sepharose and Superose 12 columns. The purified protein has a molecular mass of 68 +/- 2 kDa, as determined by SDS/PAGE and gel filtration, suggesting that the enzyme behaves as a monomer. The concentration-dependence of MAGL activity with monooleoylglycerol, the preferred substrate showed kinetics typical of an interfacial lipolytic enzyme displaying optimal activity on emulsified substrate particles; apparent Km values were 0.27 mM and 0.49 mM for the sn-1(3)- and sn-2-isomers respectively. MAGL had no, or negligible, activity towards tri-oleoylglycerol, di-oleoylglycerol, oleoylcholesterol, oleoyl-CoA and phosphatidylcholine; it was inhibited by di-isopropylfluorophosphate, PMSF and diethyl p-nitrophenyl phosphate, suggesting that MAGL is a serine hydrolase. MAGL activity was not modified by bile salt or apolipoprotein C-II, whereas a dose-dependent inhibition was observed with apolipoprotein A-I.
Carbon Nanotubes as Nanoreactors for Fabrication of Single-Crystalline Mg3N2 Nanowires (2006)

Due to fast decomposition of Mg3N2 in the presence of water in the atmosphere (Mg3N2+6H2O-->3Mg(OH)2+2NH3), the synthesis of single-crystalline Mg3N2 nanowires has been a challenge. Here, we demonstrate that carbon nanotubes may serve as nanoreactors for a simple thermal reaction process resulting in the first fabrication of high-quality, large-yield, single-crystalline Mg3N2 nanowires. The Mg3N2 nanowires are homogeneously sheathed over their entire lengths with very thin graphitic carbon tubular layers, which effectively prevent their decomposition (even when the samples are put into water or exposed to atmosphere for several months). We have systematically analyzed for the first time the Mg3N2 nanomaterial by means of transmission electron microscopy (TEM), high-resolution TEM, and electron diffraction. Successful fabrication of carbon sheath protected Mg3N2 nanowires may promote further experimental studies on their crystal structures and properties.
Surface and mRNA expression of the CD52 antigen by human eosinophils but not by neutrophils (1996)

Eosinophilic and neutrophilic granulocytes represent major effector cells in the inflammatory response. Whereas neutrophils are predominantly involved in bacterial infections, eosinophils are of essential importance in the allergic inflammation. Surface markers have been used to distinguish neutrophils (CD16+) from eosinophils (CD16-) and might indicate different functional properties of these cells. In this study, expression and functional activity of CD52 on human eosinophils and neutrophils was investigated in nonatopic healthy donors and from patients with hypereosinophilia. Flow cytometric analysis using different anti-CD52 monoclonal antibodies (MoAbs) (mouse IgG3, humanized IgG1, and rat IgM) showed significant and homogeneous expression of CD52 on human eosinophils, but not on neutrophils. In addition, reverse transcription-polymerase chain reaction and Northern blot analysis showed that CD52 mRNA was constitutively expressed in eosinophils but not in neutrophils. Furthermore, expression of CD52 could be diminished in a dose-dependent manner by preincubation of eosinophils with phosphatidylinositol-specific phospholipase C, suggesting that CD52 on eosinophils is anchored to the membrane through a glycosylphosphatidylinositol (GPI) molecule. Whereas the phorbolester phorbol myristate acetate was able to downregulate the expression of CD52 on eosinophils in a dose-dependent manner, different eosinophil activating cytokines and chemotaxins had no effect. Cross-linking of CD52 by mouse anti-CD52 MoAb (IgG3) and humanized anti-CD52 MoAb (IgG1) with goat antimouse antibody and mouse antihuman antibody, respectively, dose-dependently resulted in an inhibition of reactive oxygen species production of eosinophils after stimulation with C5a, platelet-activating factor, and granulocyte-macrophage colony-stimulating factor. In summary, this study shows that the GPI-anchored antigen CD52 is not only a useful marker to distinguish eosinophils from neutrophils. The data point out a novel role of the CD52 antigen on human eosinophils that might be of clinical relevance, because cross-linking of this molecule will stop the destructive power of human eosinophils in the inflammatory tissue.
Rab GDI: a solubilizing and recycling factor for rab9 protein. (1993)

Rab proteins are thought to function in the processes by which transport vesicles identify and/or fuse with their respective target membranes. The bulk of these proteins are membrane associated, but a measurable fraction can be found in the cytosol. The cytosolic forms of rab3A, rab11, and Sec4 occur as equimolar complexes with a class of proteins termed "GDIs," or "GDP dissociation inhibitors." We show here that the cytosolic form of rab9, a protein required for transport between late endosomes and the trans Golgi network, also occurs as a complex with a GDI-like protein, with an apparent mass of approximately 80 kD. Complex formation could be reconstituted in vitro using recombinant rab9 protein, cytosol, ATP, and geranylgeranyl diphosphate, and was shown to require an intact rab9 carboxy terminus, as well as rab9 geranylgeranylation. Monoprenylation was sufficient for complex formation because a mutant rab9 protein bearing the carboxy terminal sequence, CLLL, was prenylated in vitro by geranylgeranyl transferase I and was efficiently incorporated into 80-kD complexes. Purified, prenylated rab9 could also assemble into 80-kD complexes by addition of purified, rab3A GDI. Finally, rab3A-GDI had the capacity to solubilize rab9GDP, but not rab9GTP, from cytoplasmic membranes. These findings support the proposal that GDI proteins serve to recycle rab proteins from their target membranes after completion of a rab protein-mediated, catalytic cycle. Thus GDI proteins have the potential to regulate the availability of specific intracellular transport factors.
Proteome and glycosylation mapping identifies post-translational modifications associated with aggressive breast cancer (2001)

Changes in glycosylation of glycoproteins and glycolipids is a common feature of cancer and may influence cancer cell behaviour, perhaps by enabling cell-cell interactions which favour metastasis or by allowing cancer cells to evade immuno-surveillance. Studies to identify glycosylation changes in human cancer have often used immunohistochemical techniques with lectins or antibodies and human tissue sections. Whilst some detailed biochemical studies have been performed there are few clinically relevant studies since the numbers of specimens evaluated are often very small. Using an immuno-histochemical approach, we have found that the lectin HPA from the albumen gland of Helix pomatia detects aggressive metastatic breast cancers. We have sought to identify the breast cancer associated oligosaccharides and the proteins to which they are attached via 2-DE for proteome analysis and HPLC separations for glycosylation mapping. Sixty-nine breast cancer specimens were studied. The HPA staining pattern, clinical treatment and follow-up data were known. Oligosaccharides that related to HPA staining were identified and found in elevated levels in metastatic breast cancer specimens. Human breast and colorectal cancer cells grown in vitro and in a clinically relevant animal model of metastasis also show increased levels of the oligosaccharides. We are now structurally characterising the oligosaccharides and aim to use them as diagnostic tools and targets for immuno-therapy of breast and other solid tumours.
Cadherin-11 Promotes the Metastasis of Prostate Cancer Cells to Bone (2008)

Bone is the most common site of metastases from prostate cancer. The mechanism by which prostate cancer cells metastasize to bone is not fully understood, but interactions between prostate cancer cells and bone cells are thought to initiate the colonization of metastatic cells at that site. Here, we show that cadherin-11 (also known as osteoblast-cadherin) was highly expressed in prostate cancer cell line derived from bone metastases and had strong homophilic binding to recombinant cadherin-11 in vitro. Down-regulation of cadherin-11 in bone metastasis-derived PC3 cells with cadherin-11-specific short hairpin RNA (PC3-shCad-11) significantly decreased the adhesion of those cells to cadherin-11 in vitro. In a mouse model of metastasis, intracardiac injection of PC3 cells led to metastasis of those cells to bone. However, the incidence of PC3 metastasis to bone in this model was reduced greatly when the expression of cadherin-11 by those cells was silenced. The clinical relevance of cadherin-11 in prostate cancer metastases was further studied by examining the expression of cadherin-11 in human prostate cancer specimens. Cadherin-11 was not expressed by normal prostate epithelial cells but was detected in prostate cancer, with its expression increasing from primary to metastatic disease in lymph nodes and especially bone. Cadherin-11 expression was not detected in metastatic lesions that occur in other organs. Collectively, these findings suggest that cadherin-11 is involved in the metastasis of prostate cancer cells to bone.
A New Initiative on Precision Medicine (2015)

President Obama has announced a research initiative that aims to accelerate progress toward a new era of precision medicine, with a near-term focus on cancers and a longer-term aim to generate knowledge applicable to the whole range of health and disease.