gebhart/patrepeval huggingface dataset:
Intratumor CpG-Oligodeoxynucleotide Injection Induces Protective Antitumor T Cell Immunity (2003)

Tumor cells are typically poorly immunogenic. The same mechanisms that evolved to avoid the induction of immune responses against self tissues, and, hence, autoimmune disease, also have to be overcome for immune therapy of cancer. Toll-like receptor-activating microbial products such as CpG motif containing DNA are among the primary stimuli that the immune system uses to distinguish between infectious nonself (that is to be attacked) and noninfectious self (that must not be attacked). We tested in a murine RMA lymphoma/C57BL/6 model whether providing the infectious nonself context in a tumor-by injecting CpG-oligodeoxynucleotides directly into the tumor-would elicit a protective antitumor response. Complete remission of established solid tumors was achieved in immune competent mice, but not in T cell/B cell-deficient RAG-1 knockout mice. Intratumor injection of CpG-oligodeoxynucleotides was shown to induce a tumor-specific CD4(+) and CD8(+) T cell response of the type 1 effector class, and T cells adoptively transferred the protection to RAG-1 knockout mice. The data show that intratumor injection of CpG-oligodeoxynucleotides is a promising strategy for rendering tumors immunogenic.
Quantum-well saturable absorber at 1.55μm on GaAs substrate with a fast recombination rate (2006)

We propose and realize a structure designed for fast saturable absorber devices grown on GaAs substrate. The active region consists of a 1.55μm absorbing GaInNAsSb quantum well (QW) surrounded by two narrow QWs of GaAsN with a N concentration up to 13%. Photoexcited carriers in the GaInNAsSb QW are expected to recombine by tunneling into the wide distribution of subband gap states created in the GaAsN QW. An absorption study shows that edge energy and excitonic peak intensity of the GaInNAsSb QW are not affected by the proximity of the GaAsN QWs. Pump-probe measurements provide information on the carrier relaxation dynamics which is dependent on spacer thickness, as expected for a tunneling process. We show that this process can be enhanced by increasing the N content in the GaAsN layers. Using this design, we have realized a monolithic GaAs-based saturable absorber microcavity with a 1∕e recovery time of 12ps.
Kernel Number Determination in Argentinean Maize Hybrids Released between 1965 and 1993 (2004)

Grain yield and the stability of harvest index are greater in newer than in older Argentinean maize ( Zea mays L.) hybrids. The objective of this study was to elucidate mechanisms underlying the superior yield and harvest index stability of newer Argentinean maize hybrids using the relationship between kernel number per plant (KN P ) and plant growth rate during the period bracketing silking (PGR s ). Three experiments were performed at Balcarce, Argentina, during two growing seasons (1998–2000). Maize was grown under a wide range of plant densities (from 2 up to 30 plants m −2 ) to generate contrasting availability of resources per plant. Growth of individual plants during the period bracketing silking was estimated through a nondestructive method on the basis of relationships between actual shoot dry matter and morphometric variables, including stem and ear diameters and ear length. Detasseling and silk pollination synchronization treatments were imposed in one experiment to also modify available resources per kernel and kernel sink strength. Newer hybrids set more kernels per unit PGR s than older hybrids as is indicated by (i) the lower threshold PGR s for kernel set and (ii) greater potential kernel number at high availability of resources per plant, for newer than for older hybrids. At low and intermediate PGR s , the greater kernel set per unit PGR s in newer vs. older hybrids was attributable to greater partitioning of dry matter to the topmost ear during the period bracketing silking, whereas number of kernels set per unit of ear growth rate did not differ. In contrast, kernel set per unit of ear growth rate was greater in newer than in older hybrids when PGR s was high. Results of this study indicate that genetic yield improvement in maize is attributable, in part, to increased partitioning of dry matter to the ear during the critical period bracketing silking.
Gene Expression Patterns in Ovarian Carcinomas (2003)

We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly serous papillary) based on their gene expression patterns. The differences may yield insights into the worse prognosis and therapeutic resistance associated with clear cell carcinomas. A comparison of the gene expression patterns in the ovarian cancers to published data of gene expression in breast cancers revealed a large number of differentially expressed genes. We identified a group of 62 genes that correctly classified all 125 breast and ovarian cancer specimens. Among the best discriminators more highly expressed in the ovarian carcinomas were PAX8 (paired box gene 8), mesothelin, and ephrin-B1 (EFNB1). Although estrogen receptor was expressed in both the ovarian and breast cancers, genes that are coregulated with the estrogen receptor in breast cancers, including GATA-3, LIV-1, and X-box binding protein 1, did not show a similar pattern of coexpression in the ovarian cancers.
Ultrafast Long-Range Charge Separation in Organic Semiconductor Photovoltaic Diodes (2013)

Understanding the charge-separation mechanism in organic photovoltaic cells (OPVs) could facilitate optimization of their overall efficiency. Here we report the time dependence of the separation of photogenerated electron hole pairs across the donor-acceptor heterojunction in OPV model systems. By tracking the modulation of the optical absorption due to the electric field generated between the charges, we measure ~200 millielectron volts of electrostatic energy arising from electron-hole separation within 40 femtoseconds of excitation, corresponding to a charge separation distance of at least 4 nanometers. At this separation, the residual Coulomb attraction between charges is at or below thermal energies, so that electron and hole separate freely. This early time behavior is consistent with charge separation through access to delocalized π-electron states in ordered regions of the fullerene acceptor material.
[Endocrinological contribution for invasion and metastasis in gynecological cancers]. (1996)

The development and growth of gynecological cancers are related to steroid hormone actions. Alternatively, this prompts us to study biological contribution of sex steroids for invasion and metastasis in gynecological cancers. The first step of metastasis is the detachment of tumor cells. The adherens junction forms a main cell-to-cell junctional complex, mainly consisting of E-cadherin, alpha- and beta-catenins, etc. Estrogen suppressed the expression of their mRNAs, and the adhesive function of cells via adherens junction in endometrial cancer cells. Progestin and danazol reversed the estrogen-induced suppression. Estrogen enhanced invasiveness of endometrial cancer cells though the reconstituted basement membrane and interstitium using the Boyden chamber. Progestin reduced the estrogen-induced invasiveness. The final step of metastasis is tumor-derived neovascularization for growth of metastatic cancer cells. Progestin inhibited basic fibroblast growth factor (FGF) activity, which mainly contribute to tumor-derived neovascularization, regardless of growth-inhibition in some endometrial cancers. Progestin inhibits basic FGF in well-differentiated (WD) endometrial cancer cells, but not in poorly differentiated (PD) endometrial cancer cells. TNP470, a inhibitor of vessel endothelial proliferation, inhibited directly basic FGF in the PD. Therefore, the adequate combination therapy of progestin and TNP470 could efficiently inhibit angiogenic potential of heterologous endometrial cancers. The ratio of estrogen receptor exon 5 splicing variant (ER delta E5) to wild type-ER mRNA expression increased in some metastatic lesions of cancers. The dominant expression of ER delta E5 mRNA might be related to metastatic potential of gynecological cancers. Progesterone receptor from A (PR-A), initiated from in-frame AUG present in the PR from B (PR-B) mRNA, lacks the N-terminal 164 amino acids of PR-B, and acts as a progestin-dependent, trans-dominant repressor of PR-B function and other steroid receptor function. The expression of PR-B mRNA was dominantly expressed in all metastatic gynecological cancers given. This might be related to metastatic potential of gynecological cancers. To know tumorigenic potential of sex steroid receptors, ER, PR-A and PR-B genes were transfected to NIH3T3 cells. Transfected cells with PR-A gene alone formed a few colonies in double soft agar. On the other hand, the cells with PR-B and ER genes under the presence of estradiol formed plenty of colonies. Therefore, overexpression of PR-B under the absence of PR-A might be related to tumorigenic potential. In conclusion, estrogen could enhance some steps of metastasis in endometrial cancers, and progestin could inhibit the estrogen-induced events, regardless of growth-inhibition. Relative over-expression of ER exon 5 splicing variant, and PR-B might contribute to metastatic potential in gynecological cancers.
Antiangiogenic Strategies and Agents in Clinical Trials (2000)

The understanding that the growth of tumors depends on the acquisition of a blood supply has led to the development of new therapies for cancer and other angiogenic diseases based on inhibition of neovascularization. This review examines the role of angiogenesis in cancer progression and describes various strategies for interfering with this process. The developmental status of angiogenesis inhibitors in human clinical trials is presented, including their proposed mechanisms of action. Standard chemotherapeutic agents and angiogenesis inhibitors are compared, noting that different end points might need to be considered in clinical trials and that drug resistance may be less of a problem with antiangiogenic therapy than with conventional chemotherapy regimens. The suggestion is made that cytotoxic chemotherapy and angiogenesis inhibitors used in combination may produce complementary therapeutic benefits in the treatment of cancer.
A Genetic Analysis of Chloroplast Division and Expansion in Arabidopsis thaliana (1994)

A nuclear recessive mutant of Arabidopsis thaliana, arc5, has been isolated in which there is no significant increase in chloroplast number during leaf mesophyll cell expansion and in which there are only 13 chloroplasts per mesophyll cell compared with 121 in wild-type cells. Mature arc5 chloroplasts in fully expanded mesophyll cells are 6-fold larger than in wild-type cells. A large proportion of arc5 chloroplasts also show some degree of central constriction, suggesting that the mutation has prevented the completion of the chloroplast division process. To examine the interaction of arc loci, a double mutant was constructed between arc1, a mutant possessing many small chloroplasts, and arc5. A second double mutant was also constructed between arc3, a previously discovered mutant also possessing few large chloroplasts per cell, and arc1. Analysis of these double mutants shows that chloroplast number per mesophyll cell is greater when arc5 and arc3 mutations are expressed in the arc1 background than when expressed alone. The cell-specific nature of arc mutants was also analyzed. The phenotypic traits characteristic of arc3 and arc5 are a reduction in chloroplast number and an increase in chloroplast size in mesophyll cells: these changes are also observed in reduced form in the epidermal and guard cell chloroplasts of arc3 and arc5 plants. Analysis of parenchyma sheath cell chloroplasts suggests that in leaves of arc1 plants the normal developmental distinction between mesophyll and parenchyma sheath chloroplasts is perturbed. The relevance of these findings to the analysis of the control of chloroplast division in mesophyll cells is discussed.
Designing substrate specificity by protein engineering of electrostatic interactions. (1987)

Protein engineering of electrostatic interactions between charged substrates and complementary charged amino acids, at two different sites in the substrate binding cleft of the protease subtilisin BPN', increases kcat/Km toward complementary charged substrates (up to 1900 times) and decreases kcat/Km toward similarly charged substrates. From kinetic analysis of 16 mutants of subtilisin and the wild type, the average free energies for enzyme-substrate ion-pair interactions at the two different sites are calculated to be -1.8 +/- 0.5 and -2.3 +/- 0.6 kcal/mol (1 cal = 4.18 J) [at 25 degrees C in 0.1 M Tris X HCl (pH 8.6)]. The combined electrostatic effects are roughly additive. These studies demonstrate the feasibility for rational design of charged ligand binding sites in proteins by tailoring of electrostatic interactions.
Identification of Gene Markers Associated With Aggressive Meningioma by Filtering Across Multiple Sets of Gene Expression Arrays (2010)

Meningiomas are common intracranial tumors, but relatively little is known about the genetic events responsible for their clinical diversity. Although recent genomic studies have provided clues, the genes identified often differ among publications. We used microarray expression profiling to identify genes that are differentially expressed, with at least a 4-fold change, between grade I and grade III meningiomas. We filtered this initial set of potential biomarkers through a second cohort of meningiomas and then verified the remaining genes by quantitative polymerase chain reaction followed by examination using a third microarray expression cohort. Using this approach, we identified 9 overexpressed (TPX2, RRM2, TOP2A, PI3, BIRC5, CDC2, NUSAP1, DLG7, SOX11) and 2 underexpressed (TIMP3, KCNMA1) genes in grade III versus grade I meningiomas. As a further validation step, we analyzed these genes in a fourth cohort and found that patients with grade II meningiomas with high topoisomerase 2-α protein expressions (>5% labeling index) had shorter times to death than patients with low expressions. We believe that this multistep multi-cohort approach provides a robust method for reducing false-positives while generating a list of reproducible candidate genes that are associated with clinically aggressive meningiomas and are suitable for analysis for their potential prognostic value.
Changing Epidemiology of S. aureus Infections in the U.S. (2012)

The emergence of the USA300 strain as an important cause of community-onset methicillin-resistant Staphylococcus aureus (MRSA) infections in the late 1990s and early 2000s profoundly changed the epidemiology of staphylococcal disease, both in the U.S. and worldwide. Although several recent studies have suggested that the incidence of healthcare-associated and hospital-onset MRSA infections may be decreasing, less …
Role of antigen selectivity in autoimmune responses to the Ku (p70/p80) antigen. (1989)

Levels of anti-Ku (p70/p80) antibodies were measured longitudinally in sera from four individuals with systemic lupus erythematosus or related disorders. Antibodies to the native Ku antigen (p70/p80 complex) varied over a range of up to 577-fold. Large fluctuations were also observed in the levels of autoantibodies to several distinct epitopes of the Ku (p70/p80) antigen. Levels of these individual autoantibody populations generally paralleled one another, suggesting that they are coordinately regulated. A similar pattern of anti-DNA antibody fluctuation was seen in some sera. To examine the possibility that these autoantibodies were generated by polyclonal B cell activation, the levels of anti-Ku (p70/p80) and anti-DNA antibodies were compared to the levels of antibodies to Escherichia coli proteins, tetanus toxoid, and bovine insulin, transferrin, cytochrome c, serum albumin, and thyroglobulin. In sera from the same individual, anti-Ku (p70/p80) antibodies were sometimes produced in the complete absence of polyclonal activation, and at other times were accompanied by increased polyclonal activation. Anti-DNA antibody levels more closely paralleled the level of polyclonal activation than did the anti-Ku (p70/p80) levels. These studies suggest that anti-Ku (p70/p80) antibodies are generated by an antigen-selective mechanism, but that polyclonal activation frequently, although not invariably, accompanies autoantibody production. This observation is consistent with the possibility that polyclonal activation might be secondary to autoantibody production.
Restriction endonuclease analysis of members of the Mycobacterium avium-M. intracellulare-M. scrofulaceum serocomplex (1987)

Organisms belonging to the Mycobacterium avium-M. intracellulare-M. scrofulaceum (MAIS) serocomplex were subjected to restriction endonuclease analysis (REA) with the enzymes BstEII, PvuII, and BclI. Substantial genetic heterogeneity was observed between members of an authenticated collection of the 31 serotypes. Serotypes 2 and 3 were indistinguishable, however, as were serotypes 5 and 10. No direct correlation could be made between restriction pattern and species identification. REA of serotype 2 and serotype 8 isolates from various geographic locations and animal origins showed that, within limits, the restriction pattern could be used as an index of serotype. Some isolates that were unable to be classified serologically exhibited restriction patterns identical to those of strains that were able to be classified by seroagglutination. The difficulty of interpreting much of the epidemiological data concerning MAIS organisms may be partially explained by the extent of heterogeneity observed by REA. These findings support the contention that the MAIS complex has a substantially greater degree of heterogeneity than has been revealed by traditional methods.
Collabot (2018)

In recent years, enterprise group chat collaboration tools, such as Slack, IBM»s Watson Workspace and Microsoft Teams, have presented unprecedented growth. With all the potential benefits of these tools - productivity increase and improved group communication - come significant challenges. Specifically, the 'always on' feature that makes it hard for users to cope with the load of conversational content and get up to speed after logging off for a while. In this demo, we present Collabot - a chat assistant service that implicitly learns users interests and social ties within a chat group and provides a personalized digest of missed content. Collabot assists users in coping with chat information overload by helping them understand the main topics discussed, collaborators, links and resources. This demo has two main contributions. First, we present a novel personalized group chat summarization algorithm; second the demonstration depicts a working implementation applied on different chat groups from different domains within IBM. A video, describing the demo can be found at https://www.youtube.com/watch?v=6cVsstiJ9vk.
A Simple Fabrication Process Based on Micro-masonry for the Realization of Nanoplate Resonators with Integrated Actuation and Detection Schemes (2016)

In this work, we use the micro-masonry technique to fabricate nanoplate resonators with integrated electrostatic actuation and capacitive detection in a few steps. Our approach is an alternative solution to the current fabrication methods used to create membranes and plates that usually rely on the selective etching of a sacrificial layer. Highly doped silicon plates were transfer-printed using microtip elastomeric stamps onto insulated bases displaying cavities in order to form suspended structures with airtight gaps. By post-processing adequate interconnections, the fabricated resonators were actuated and their resonant frequency measured in a fully integrated manner. The tested nanoplate devices behave as predicted by theory and offer quality factors of more than 30 in air. Because the cavities used for electrostatic actuation/sensing of the devices are tight sealed, nanoplates fabricated via micro-masonry are suitable for liquid environment operation and are thus a promising solution for biosensing applications.
Letermovir (2013)

Novel therapies are urgently needed for the management of cytomegalovirus (CMV) disease in high-risk patients. Currently licensed agents target the viral DNA polymerase, and although they are effective, they are fraught with toxicities to patients. Moreover, emergence of antiviral resistance is an increasing problem, particularly for patients on long-term suppressive therapy. A new agent, letermovir (AIC246), shows great promise for the management of CMV infection. Advantages include its good oral bioavailability, its lack of toxicity, and the apparent absence of drug-drug interactions. Letermovir has a novel mechanism of action, exerting its antiviral effect by interfering with the viral pUL56 gene product and in the process disrupting the viral terminase complex. This agent demonstrates substantial promise as an alternative to more toxic antivirals in patients at high risk for CMV disease, particularly in the transplantation setting.
A focal adhesion protein‐based mechanochemical checkpoint regulates cleft progression during branching morphogenesis (2011)

Cleft formation is the initial step of branching morphogenesis in many organs. We previously demonstrated that ROCK 1 regulates a nonmuscle myosin II-dependent mechanochemical checkpoint to transition initiated clefts to progressing clefts in developing submandibular salivary glands. Here, we report that ROCK-mediated integrin activation and subsequent formation of focal adhesion complexes comprise this mechanochemical checkpoint. Inhibition of ROCK1 and nonmuscle myosin II activity decreased integrin β1 activation in the cleft region and interfered with localization and activation of focal adhesion complex proteins, such as focal adhesion kinase (FAK). Inhibition of FAK activity also prevented cleft progression, by disrupting recruitment of the focal adhesion proteins talin and vinculin and subsequent fibronectin assembly in the cleft region while decreasing ERK1/2 activation. These results demonstrate that inside-out integrin signaling leading to a localized recruitment of active FAK-containing focal adhesion protein complexes generates a mechanochemical checkpoint that facilitates progression of branching morphogenesis.
High aspect ratio submicron silicon pillars fabricated by photoassisted electrochemical etching and oxidation (1995)

A technique for fabricating submicron free-standing silicon pillars has been developed. The silicon pillars have a high packing density, and aspect ratios over 50:1 can easily be achieved. Photoassisted electrochemical etching in hydrofluoric acid is used to etch deep macropores in n-type silicon wafers which have been patterned by standard photolithography. The regular macropores can be used for fabricating photonic band-gap structures. The bulk silicon remaining between the close-packed macropores is oxidized. Free-standing pillars are then formed by subsequently wet etching the silicon dioxide. The pillars are the initial structures for forming quantum wires using further oxidation and etch steps.