gebhart/patrepeval huggingface dataset:
Sequence of the cDNA encoding the laminin B1 chain reveals a multidomain protein containing cysteine-rich repeats. (1987)

Laminin is a basement membrane-specific glycoprotein (800 kDa) consisting of three chains: A, B1, and B2. Laminin has diverse biological functions, which include stimulating epithelial cell growth and differentiation. We have isolated two overlapping cDNA clones that span 5.9 kilobases and code for the entire B1 chain of mouse laminin. The nucleotide sequence of the clones reveals a 5358-base pair open reading frame that potentially codes for 1786 amino acids, including 20 amino acids of a presumptive signal peptide. Analysis of the deduced protein sequence predicts that the B1 chain has seven distinct domains that include cysteine-rich repeats, alpha-helical, and globular structures. Part of the cysteine-rich region is homologous to epidermal growth factor and other proteins that contain epidermal growth factor-like repeats.
Probabilistic information retrieval approach for ranking of database query results (2006)

We investigate the problem of ranking the answers to a database query when many tuples are returned. In particular, we present methodologies to tackle the problem for conjunctive and range queries, by adapting and applying principles of probabilistic models from information retrieval for structured data. Our solution is domain independent and leverages data and workload statistics and correlations. We evaluate the quality of our approach with a user survey on a real database. Furthermore, we present and experimentally evaluate algorithms to efficiently retrieve the top ranked results, which demonstrate the feasibility of our ranking system.
A methodology for the systematic and quantitative study of cell contact guidance in oriented collagen gels Correlation of fibroblast orientation and gel birefringence (1993)

Despite the likely role of contact guidance in every physiological process involving cell migration, its study in a three-dimensional tissue-equivalent environment has been precluded, heretofore, by inherent difficulties in systematically preparing well-defined contact guidance fields and quantifying the resultant contact guidance. Here, we describe a novel use of a magnetic field to orient collagen fibrils during fibrillogenesis, entrapping cells dispersed in the collagen solution. Using computer-controlled staging and image analysis, we show from automated birefringence measurements of the resultant slab of cell-populated gel contained in a specially designed observation chamber that the fibril orientation is biased along the long axis of the chamber uniformly throughout the chamber. Further, we show that the degree of fibril orientation, and consequently the elicited contact guidance, can be controlled by independently varying the magnetic field strength or temperature during fibrillogenesis. We characterize the contact guidance response to the imposed contact guidance field by measuring cell orientation relative to the axis of fibril orientation from still images obtained in time-lapse via automated image analysis. We present the first quantitative correlation of contact guidance (based on cell orientation) with collagen fibril orientation (based on birefringence) for human foreskin fibroblasts cultured in a collagen gel, by using gels of varying orientation resulting from different magnetic field strengths and temperatures during fibrillogenesis, and by using sufficiently low cell concentrations and early observation times.
Functional Gene Expression Analysis Uncovers Phenotypic Switch in Aggressive Uveal Melanomas (2006)

Microarray gene expression profiling is a powerful tool for generating molecular cancer classifications. However, elucidating biological insights from these large data sets has been challenging. Previously, we identified a gene expression-based classification of primary uveal melanomas that accurately predicts metastatic death. Class 1 tumors have a low risk and class 2 tumors a high risk for metastatic death. Here, we used genes that discriminate these tumor classes to identify biological correlates of the aggressive class 2 signature. A search for Gene Ontology categories enriched in our class-discriminating gene list revealed a global down-regulation of neural crest and melanocyte-specific genes and an up-regulation of epithelial genes in class 2 tumors. Correspondingly, class 2 tumors exhibited epithelial features, such as polygonal cell morphology, up-regulation of the epithelial adhesion molecule E-cadherin, colocalization of E-cadherin and beta-catenin to the plasma membrane, and formation of cell-cell adhesions and acinar structures. One of our top class-discriminating genes was the helix-loop-helix inhibitor ID2, which was strongly down-regulated in class 2 tumors. The class 2 phenotype could be recapitulated by eliminating Id2 in cultured class 1 human uveal melanoma cells and in a mouse ocular melanoma model. Id2 seemed to suppress the epithelial-like class 2 phenotype by inhibiting an activator of the E-cadherin promoter. Consequently, Id2 loss triggered up-regulation of E-cadherin, which in turn promoted anchorage-independent cell growth, a likely antecedent to metastasis. These findings reveal new roles for Id2 and E-cadherin in uveal melanoma progression, and they identify potential targets for therapeutic intervention.
Facing up to Membranes: Structure/Function Relationships in Phospholipases (1987)

Phospholipases are unique enzymes in that they have evolved to attack aggregated substrates (e.g., phospholipids in a membrane). Only a trace of their full activity is exhibited against monomerically dispersed phospholipids. Moreover, phospholipase activity can be “tuned” by structural factors operating within the aggregate. These include steric influences on the head groups, hydration of the polar regions, chain-packing density, surface charge, and surface defects, all of which contribute to the physical state of the interfacial region (for review, see Israelachvili et al. 1980). Furthermore, perturbation of lamellar aggregates by insertion of amphipathic proteins may modulate phospholipase activity. For example, amphipathic peptides such as melittin from bee venom (Vogel 1981), cardiotoxins from some snake (Elapidae) venoms (Louw and Visser 1978), and polymixin B (bacterial), which are known to insert into phospholipid bilayers, increase the activity of extracellular phospholipases A2 toward phospholipid vesicles, liposomes (Yunes et al. 1977), and cell membranes (Tönsing...
Decay accelerating factor (CD55): a target for cancer vaccines? (1999)

The 791Tgp72 antigen has been used successfully as a target for tumor imaging and T-cell immunotherapy. We have characterized this antigen using the monoclonal antibody 791T/36 as a 72/66 kDa doublet. NH2-terminal protein sequencing of the two bands revealed identity with the complement regulatory protein CD55. Antibodies recognizing different domains of CD55 were also shown to bind to the purified 791Tgp72, although sequence analysis of the cDNA cloned from 791T tumor cells showed 100% homology with CD55 and transfection of the cDNA into antigen-negative CHO cells resulted in binding of 791T/36. This identifies the tumor antigen 791Tgp72 as CD55. This protein protects cells from complement attack; however, it can also transduce signals in lymphocytes and is a ligand for CD97, expressed by activated T cells. These results suggest that CD55 plays a role in signaling between the innate and adaptive immune responses. It is therefore a very intriguing target, because absence of the molecule makes the tumor cells susceptible to complement, whereas protective overexpression results in the antigen being a target for T-cell immunotherapy.
Protection of marmoset monkeys against EAE by treatment with a murine antibody blocking CD40 (mu5D12) (2002)

CD40-CD40 ligand interactions are crucial to cognate interactions between T cells, B cells and antigen-presenting cells (APC), and contribute to non-antigen-specific effector functions of APC in inflammatory disorders. Here we demonstrate that functional blockade of CD40 with an antagonist mouse anti-human CD40 monoclonal antibody (mAb mu5D12) effectively prevents clinical expression of chronic demyelinating experimental autoimmune encephalomyelitis (EAE) in outbred marmoset monkeys, a preclinical model of multiple sclerosis. Anti-CD40 mAb interfered with development of clinical symptoms of marmoset EAE during the treatment period, even when treatment was started several weeks after T cell priming. Magnetic resonance imaging demonstrated inflammatory activity in the brain at initiation of antibody treatment, confirming that treatment interfered with the disease process. Access of therapeutic anti-CD40 to potential sites of action, the secondary lymphoid organs and the brain white matter lesions, was visualized in situ. The present data are the first to demonstrate the clinical potential of blocking APC and effector cell functions using murine antagonist anti-CD40 mAb in the treatment of chronic inflammatory diseases.
Intramolecular Reactions. V. Factors Affecting the Yield in Diazonium Cyclization Reactions1 (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntramolecular Reactions. V. Factors Affecting the Yield in Diazonium Cyclization Reactions1DeLos F. DeTar and Thomas E. WhiteleyCite this: J. Am. Chem. Soc. 1957, 79, 10, 2498–2502Publication Date (Print):May 1, 1957Publication History Published online1 May 2002Published inissue 1 May 1957https://doi.org/10.1021/ja01567a039RIGHTS & PERMISSIONSArticle Views190Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (634 KB) Get e-Alerts Get e-Alerts
The Crucial ligaments : diagnosis and treatment of ligamentous injuries about the knee (1994)

The unstable knee / The ACL deficient knee SECTION 1 CASE STUDIES SECTION 2 HISTORY EVOLUTION. EPIDEMIOLOGY: The ACL: a historical review / An evolutionary perspective / Epidemiology of the ACL / Evolution of lesions and symptoms after ACL injury. SECTION 3 ANATOMY, KINEMATICS: Anatomy of the cruciate ligaments / Fiber recruitment of the cruciate ligaments / A biomechanical function of the ACL: prevention of Medial translation of the tibia / Biomechanical concepts involved gait analysis: clinical application for the reconstructed knee / Posterior meniscal capsuloligamentous complexes of the knee / Injury to the medial capsoligamentous complex / Patellar instability: an anatomoradiographic analysis. SECTION 4 DIAGNOSIS: Diagnosis of knee ligament injuries: biomechanical precepts / Diagnosis of knee ligament inches: tests and measurement of knee motion limits / Pivot shift / Imaging / Stressradiography of the knee joint: measurements of knee motion limits in the frontal and sagittal planes / Arthroscopy: defining and treating cruciate ligament injuries. SECTION 5 NATURAL HISTORY, PREVENTION, COUNSELLING: The torn ACL: natural history of untreated lesions and rationale for selective treatment / Prevention of cruciate ligament injuries / Counselling patients with career-ending injuries. SECTION 6 SURGICAL TREATMENT: Open ACL reconstruction with patellar tendon and interference screw fixation / Arthroscopic cruciate repair and reconstruction: an overview and descriptions of technique / Arthroscopically monitored ACL reconstruction: compaction drilling and compression screw fixation / Isometric placement of cruciate ligament / Surgical repair of acute and chronic lesions of the lateral capsular ligamentous complex of the knee / Allografts in knee ligament reconstruction / The ligament augmentation device / Roof impingement of ACL grafts: diagnosis, cause, prevention and late surgical correction / ACL deficiency in children. SECTION 7 SEQUELAE: Knee ligaments in osteoarthritis of the knee / The meniscus in the ACL-deficient knee / Revision ACL surgery: evaluation and treatment. SECTION 8 REHABILITATION: Counteracting muscle atrophy after ACL injury: scientific bases for a rehabilitation program / Clinical development of preoperative and postoperative ACL rehabilitation / Continuous passive motion in postoperative knee rehabilitation / ACL injuries in the elite skier / Special techniques in rehabilitation. SECTION 9 PROSTHETIC LIGAMENTS: Prosthetic replacement of knee ligaments: overview / ACL reconstruction with Gore-Tex compact diameter ligament / Laboratory studies of biodegadable materials for cruciate ligament reconstruction / Glossary / Index.
J . M . R . 렌츠의 희극 『 가정교사 』 에 나타난 슈투름 운트 드랑의 미학 (2000)

In der letzten Zeit wurden die Dramen von J.M.R. Lenz meistens unter gesellschaftskritischen Blickwinkel betrachtet. Seine Komo¨die Der Hofmeister war auch keine Ausnahme. Wegen seiner zahlreichen gesellschaftspolitischen Schriften ist man geneigt, seine ganzen Werke auf die Widerspru¨chlichkeit der Sta¨ndegesellschaft zu beziehen. obwohl Lenz viele a¨sthetische Schriften verfast hat. Durch die repra¨sentativen dramentheoretischen Schriften Anmerkungen u¨bers Theater and Rezension des Neuen Menoza stellt er neue Aspekte des Dramas. vor allem die Komo¨die in den Vordergrund. Durch die na¨here Analyse seiner Theorie kann man ganz anders als bisher einen neuen Interpretationsansatz fu¨r seine Dramen verwenden. Nach ihm ist die Komo¨die ein Bild der menschlichen Gesellschaft. Diese Definition bezieht sich auf eine realita¨tsnahe Darstellung der menschlichen Gesellschaft. Seine Komo¨die hat also mit dem fu¨r die herko¨mmliche HIassifikation des Dramas wichtigen Element $quot;Lachen$quot; wenig zu tun. Bei ihm gilt die traditionelle Trago¨die als die ernst haftere Komo¨die. Seine Komo¨die entha¨lt gewissermasen das Komische and das Tragische zugleich, genauso wie die Gesellschaft aus den unterschiedlichsten Elementen besteht. Wenn das Theaterstu¨ck die Tragik and die Komik in einem zeigt, dann fu¨hlen sich weder die oberen noch die niederigen Sta¨nde ausgeschlossen, denn die beiden Schichten ko¨nnen dabei die ihr passenden Elemente der menschlichen Gesellschaft unmittelbar erleben. Die tragikomischen Elemente im Werk Der Hofmeister ko¨nnen auch in diesem Sinne interpretiert werden. Dieses Werk spiegelt die Gesellschaft umfassend wider, aber nicht im Sinne einer Gesellschaftskritik, sondern in der Absicht des Autors. der durch die Einbeziehung aller gesellschaftlichen Elemente das Theater fair jedermann schaffen will. Lenz nennt die Komo¨die die Vorstellung fu¨r jedermann, denn er will, nach meiner Meinung, das Sympathie and Versta¨ndnis fu¨r die jeweils andere Schicht entsteht. Auf diese Weise ko¨nnen Spannungen gelo¨st werden und die Gesellschaft a¨sthetisch zusammengefu¨hrt werden. Daher kann man das Werk Der Hofmeister ganz anders als die meisten Forschungsrichtungen rein a¨sthetisch interpretieren.
Belief Propagation for Weighted b-Matchings on Arbitrary Graphs and its Relation to Linear Programs with Integer Solutions (2011)

We consider the general problem of finding the minimum weight -matching on arbitrary graphs. We prove that, whenever the linear programming (LP) relaxation of the problem has no fractional solutions, then the belief propagation (BP) algorithm converges to the correct solution. We also show that when the LP relaxation has a fractional solution then the BP algorithm can be used to solve the LP relaxation. Our proof is based on the notion of graph covers and extends the analyses of [M. Bayati, D. Shah and M. Sharma, in Proceedings of the IEEE Int. Symp. Information Theory, 2005] and [B. Huang and T. Jebara, in Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics, 2007]. The result is notable in the following regards: (1) It is one of a very small number of proofs showing correctness of BP without any constraint on the graph structure; (2) Variants of the proof work for both synchronous and asynchronous BP; it is the first proof of convergence and correctness of an asynchronous BP algorithm for a combinatorial optimization problem.
Selective Synthesis of Chlorohydrogermanes from Mono-, Di-, and Trihydrogermanes (2001)

Abstract Treatment of hydrogermanes, R4−nGeHn (R = Hex, Et, Ph, n = 1–3), with 2 equiv of CuCl2 in ether at room temperature or in toluene under reflux led to selective replacement of an H–Ge bond with a Cl–Ge bond, giving the corresponding chlorohydrogermanes, R4−nGeHn−1Cl, selectively.
Dual control of myc expression through a single DNA binding site targeted by ets family proteins and E2F-1. (1994)

NIH3T3 cells expressing a mutant colony-stimulating factor-1 receptor (CSF-1R) containing a phenylalanine for tyrosine substitution in the tyrosine kinase domain at codon 809 exhibit defective myc regulation and do not enter S phase when stimulated by CSF-1. Enforced expression of either ets-1 or ets-2 in these cells restores their mitogenic response, albeit less efficiently than myc itself, suggesting that ets proteins may regulate c-myc expression. Ets-1 transactivates reporter genes driven by the human and mouse c-myc promoters through the binding site for the transcription factor E2F, the latter being required for E1A- and serum-induced c-myc expression. Analysis of E2F-1 sequences identified a minimal DNA binding domain that is related to those of ets proteins. Although E2F and ets proteins interact with similar consensus DNA binding sites, in vitro binding assays revealed that E2F can bind DNA as a homodimer, whereas ets proteins bind these sites as monomers. E2F and ets proteins do not form heterodimers in vitro and do not transactivate c-myc synergistically. Thus, E2F-1 and ets family members may independently regulate c-myc transcription through the same binding site at different times following growth factor stimulation.
Lineage Allocation During Early Embryogenesis: Mapping of the Neural Primordia and Application to the Analysis of Mouse Mutants (2003)

The methods outlined in this chapter discuss a range of techniques that have been employed for lineage analysis studies of the neural primordia from the onset of gastrulation and during neurulation. As the mouse has been extensively mapped, lineage analysis during normal morphogenesis is well understood. Attention is now focused on the tissue interactions that are essential for gastrulation and neurulation to proceed normally. The key to understanding these tissue interactions lies in the study of mutant embryos where abnormal development of specific tissue types affects the processes of gastrulation and neurulation. Lineage analysis and tissue potency experiments on particular mutant embryos will provide insight into these essential tissue interactions. As the first step toward undertaking such analysis of the neural derivatives, we have outlined the mutant strains available and detailed a protocol for the introgression of the lacZ transgene onto the mutant background.
Limitations of Genotyping Based on Amplicon Melting Temperature (2001)

cific bias" and "random patient interferences". We considered the latter two sources of error to be outside the scope of our study, in part because it is difficult to know how one might model the interferences. We did, however, discuss the importance of the continuing efforts of manufacturers to design instruments that avoid sources of error, such as those encountered by patients with special needs.
Graph-Based Semantics of the .NET Intermediate Language (2007)

The semantics of a programming language are often described in a natural language. Such descriptions are often ambiguous and hard (or even impossible) to construct in a precise way. To tackle these problems one could specify a formal description of the semantics by using a mathematical model. In this report such a mathematical model is presented for the .NET Intermediate Language (IL) in the form of graphs and transformations to these graphs. In order to be able to perform transformations on graphs, we need a start graph. The .NET Intermediate Language generates bytecode and cannot supply such a start graph. Therefore we have constructed a translator that translates an arbitrary IL program into a so called Abstract Syntax Graph (ASG). The ASG is the start graph to which we now can apply graph transformations.
Central in this report are graph production rules that we have specified in order to describe the semantics of .NET IL instructions. These production rules are used for transforming graphs, and by applying them to the (intermediate) graphs repeatedly it is possible to simulate a program. Although further research is necessary, we believe this project provides a promising basis of
representing the semantics of the .NET Intermediate Language in an intuitive and formal way.
WNT5A induces release of exosomes containing pro-angiogenic and immunosuppressive factors from malignant melanoma cells (2014)

These data indicate that WNT5A has a broader function on tumor progression and metastatic spread than previously known; by inducing exosome-release of immunomodulatory and pro-angiogenic factors that enhance the immunosuppressive and angiogenic capacity of the tumors thus rendering them more aggressive and more prone to metastasize.
Association testing of copy number variants in schizophrenia and autism spectrum disorders (2012)

These findings suggest that although CNV loci notably overlap between autism and schizophrenia, the degree of strongly statistically supported overlap in specific CNVs at these loci remains limited. These analyses also suggest that relatively severe premorbidity to CNV-associated schizophrenia in children may sometimes be diagnosed as autism spectrum disorder.