gebhart/patrepeval huggingface dataset:
A gene encoding for an α‐amylase from thermophilic Bacillus sp. strain TS‐23 and its expression in Escherichia coli (1997)

An alpha-amylase gene from Bacillus sp. strain TS-23 was cloned and expressed by using its own promoter on the recombinant plasmid pTS917 in Escherichia coli. A cell fractionation experiment revealed that approximately 60% of the amylase activity was in the periplasmic space. Analysis and activity staining of the concentrated supernatant fraction by SDS-polyacrylamide gel electrophoresis showed an apparent protein band with a mol. wt of approximately 65,000. The amylase gene (amyA) consisted of an open reading frame of 1,845 bp encoding a protein of 613 amino acids with a calculated mol. wt of 69,543. The predicted amino acid sequence showed high homology with Bacillus species, E. coli and Salmonella typhimurium alpha-amylases. Deletion of 96 amino acids from the C-terminal portion of the amylase did not result in the loss of amylolytic activity. The truncated amylase, deletion of the first 50 amino acids from the N-terminus, was overexpressed in E. coli system and refolded to yield an activable enzyme.
Electrokinetic patterning of colloidal particles with optical landscapes (2008)

We demonstrate an opto-electrokinetic technique for non-invasive particle manipulation on the surface of a parallel-plate indium tin oxide (ITO) electrode that is biased with an alternating current (AC) signal and illuminated with near-infrared (1064 nm) optical landscapes. This technique can generate strong microfluidic vortices at higher AC frequencies (>100 kHz) and dynamically and rapidly aggregate and pattern particle groups at low frequencies (<100 kHz).
Creutzfeldt-Jakob disease in a recipient of human pituitary-derived gonadotrophin: a second case. (1992)

A 44 year old female presented with a progressive cerebellar disturbance approximately 13 years after receiving human pituitary derived gonadotrophin injections as a treatment for infertility. The patient died approximately nine months later. Creutzfeldt-Jakob disease was confirmed at necropsy. This is the second reported case of Creutzfeldt-Jakob disease in a recipient of human derived gonadotrophin.
The simulation and evaluation of dynamic voltage scaling algorithms (1998)

The reduction of energy consumption in microprocessors can be accomplished without impacting the peak performance through the use of dynamic voltage scaling (DVS). This approach varies the processor voltage under software control to meet dynamically varying performance requirements. This paper presents a foundation for the simulation and analysis of DVS algorithms. These algorithms are applied to a benchmark suite specifically targeted for PDA devices.
Intellectual property issues of immune checkpoint inhibitors (2015)

Immune checkpoint inhibitors are drugs that interfere with tumor escape responses. Some members of this class are already approved, and expected to be blockbusters in the future. Many companies have developed patent activities in this field. This article focuses on the patent landscape, and discusses key players and cases related to immune checkpoint inhibitors.
The Molecular Biology of Rotaviruses. VI. RNA Species-specific Terminal Conservation in Rotaviruses (1983)

The use of T1 RNase fingerprinting of terminally labelled genomic double-stranded RNA species from various rotavirus isolates, to analyse the near terminal G-residue positions, has revealed an RNA species-specific fingerprint pattern covering approximately 40 nucleotides at the termini. These RNA species-specific terminal fingerprint patterns were found to be conserved in both rotavirus RNAs isolated from various animal species, and in isolates from a single animal species where gross divergence of internal RNA sequence for a particular RNA species was evident. This conservation of near terminal G-residue positions suggests that, internal to the short regions of absolute terminal sequence conservation that we have previously shown to be present on all rotavirus RNA species, there is a region of conserved sequence which is specific for a particular RNA species.
Surface-emitting lasers with GaAlAs/AlAs DBR grown by OMVPE (1988)

The performance of surface-emitting (SE) lasers with a Ga/sub 0.9/Al/sub 0.1/As/AlAs multilayer Bragg reflector grown by OMVPE (organometallic vapor-phase epitaxy) has been investigated. The reflectivity was 94% at a wavelength of 0.88 mu m, which is the lasing wavelength of the GaAs/GaAlAs SE laser. No sophisticated etching process for the GaAs substrate was necessary for inside mirror formation. An Au/SiO/sub 2/ semitransparent mirror, the reflectivity and transparency of which are about 94 and 3%, respectively, was used for a p-side reflector. Operating under a room-temperature pulsed condition, the lasers have a minimum threshold current of 95 mA and a lasing wavelength of 883 nm. The spectrum at I/I/sub th/=0.99 has two peaks. One, around 883 nm, is a lasing longitudinal mode, and the other, a small peak at around 870 nm, is a nonlasing neighboring longitudinal mode. Thus the longitudinal mode spacing is about 13 nm. Single-mode operation up to 1.22 times the threshold value was obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RB and c-Myc Activate Expression of the E-Cadherin Gene in Epithelial Cells through Interaction with Transcription Factor AP-2 (1998)

E-cadherin plays a pivotal role in the biogenesis of the first epithelium during development, and its down-regulation is associated with metastasis of carcinomas. We recently reported that inactivation of RB family proteins by simian virus 40 large T antigen (LT) in MDCK epithelial cells results in a mesenchymal conversion associated with invasiveness and a down-regulation of c-Myc. Reexpression of RB or c-Myc in such cells allows the reexpression of epithelial markers including E-cadherin. Here we show that both RB and c-Myc specifically activate transcription of the E-cadherin promoter in epithelial cells but not in NIH 3T3 mesenchymal cells. This transcriptional activity is mediated in both cases by the transcription factor AP-2. In vitro AP-2 and RB interaction involves the N-terminal domain of AP-2 and the oncoprotein binding domain and C-terminal domain of RB. In vivo physical interaction between RB and AP-2 was demonstrated in MDCK and HaCat cells. In LT-transformed MDCK cells, LT, RB, and AP-2 were all coimmunoprecipitated by each of the corresponding antibodies, and a mutation of the RB binding domain of the oncoprotein inhibited its binding to both RB and AP-2. Taken together, our results suggest that there is a tripartite complex between LT, RB, and AP-2 and that the physical and functional interactions between LT and AP-2 are mediated by RB. Moreover, they define RB and c-Myc as coactivators of AP-2 in epithelial cells and shed new light on the significance of the LT-RB complex, linking it to the dedifferentiation processes occurring during tumor progression. These data confirm the important role for RB and c-Myc in the maintenance of the epithelial phenotype and reveal a novel mechanism of gene activation by c-Myc.
Implementation, calibration and accuracy testing of an image-enhanced endoscopy system (2002)

This paper presents a new method for image-guided surgery called image-enhanced endoscopy. Registered real and virtual endoscopic images (perspective volume renderings generated from the same view as the endoscope camera using a preoperative image) are displayed simultaneously; when combined with the ability to vary tissue transparency in the virtual images, this provides surgeons with the ability to see beyond visible surfaces and, thus, provides additional exposure during surgery. A mount with four photoreflective spheres is rigidly attached to the endoscope and its position and orientation is tracked using an optical position sensor. Generation of virtual images that are accurately registered to the real endoscopic images requires calibration of the tracked endoscope. The calibration process determines intrinsic parameters (that represent the projection of three-dimensional points onto the two-dimensional endoscope camera imaging plane) and extrinsic parameters (that represent the transformation from the coordinate system of the tracker mount attached to the endoscope to the coordinate system of the endoscope camera), and determines radial lens distortion. The calibration routine is fast, automatic, accurate and reliable, and is insensitive to rotational orientation of the endoscope. The routine automatically detects, localizes, and identifies dots in a video image snapshot of the calibration target grid and determines the calibration parameters from the sets of known physical coordinates and localized image coordinates of the target grid dots. Using nonlinear lens-distortion correction, which can be performed at real-time rates (30 frames per second), the mean projection error is less than 0.5 mm at distances up to 25 mm from the endoscope tip, and less than 1.0 mm up to 45 mm. Experimental measurements and point-based registration error theory show that the tracking error is about 0.5-0.7 mm at the tip of the endoscope and less than 0.9 mm for all points in the field of view of the endoscope camera at a distance of up to 65 mm from the tip. It is probable that much of the projection error is due to endoscope tracking error rather than calibration error. Two examples of clinical applications are presented to illustrate the usefulness of image-enhanced endoscopy. This method is a useful addition to conventional image-guidance systems, which generally show only the position of the tip (and sometimes the orientation) of a surgical instrument or probe on reformatted image slices.
Dialektische Psychologie und Psychoanalyse (1993)

Die Gründe für die bisherige Spaltung zwischen Psychoanalyse und Hochschulpsychologie in Deutschland werden zum einen in der mangelnden Auseinandersetzung mit der Nazi-Zeit gesehen, zum anderen in unterschiedlichen Wissenstypen, die man als dialektisch reflexiv versus statisch nomologisch bezeichnen kann. Die Kluft überbrücken könnte eine "dialektische Psychologie", die wegen ihrer Behinderungen durch die herrschenden Dogmen in Ost und West historisch bis jetzt jedoch nur in wenigen Ansätzen hervorgetreten ist. Für eine fruchtbare Verbindung von kognitiver Psychologie (Piagetscher Prägung) beispielsweise und Psychoanalyse muß die implizite Dialektik dieser (und anderer) Ansätze begriffen und explizit ausformuliert werden. Nur so nimmt die Psychologie allmählich die Form eines selbstreflexiven und dialektischen Wissens an, das für die Bewältigung der enormen Herausforderungen der psychologischen und psychotherapeutischen Praxis so dringend benötigt wird.
Super-Motifs of Leucine-Rich Repeats (LRRs) Proteins (2000)

Leucine-richrepeats(LRRs)arepresentinovertwohundredsdiﬀerentproteins.Theyarepresentinorganismsthatrangefrombacteriatoman.Theyincludehormonereceptors,tyrosinekinaserecep-tors,cell-adhesionmolecules,bacterialvirulencefactors,enzymes,andextracellularmatrixbindingglycoproteins. AlloftheLRRproteinsappeartobeinvolvedinprotein-proteininteractions;theseinvolvesignaltransduction,celladhesion,DNArepair,recombination,transcription,RNAprocessing,diseaseresistance,andicenucleation[3,4].TheevolutionofLRRsisnotwellunderstood.ItisnotevenknownwhetherallLRRsshareacommonancestor.TheLRRsareusuallypresentintandem.ThemostcommonlengthoftheLRRmotifis24residues,butthelengthsofLRRrangefrom20to30.AllLRRsmotifsaredividedintoahighlyconservedpartandavariablepart[2,6].Thehighlyconservedpartconsistsofa11-residuestretch,LxxLxLxxNxL,ora12-residuestretch,LxxLxLxxCxxL,inwhich“L”isVal,Leu,orIle,“N”isAsn,Thr,Ser,orCys,and“Cys”isCysorSer[6].RecentlyitwasproposedthatLRRproteinscanbesubdividedintoatleastsixorsevensubfamilies,characterizedbydiﬀerentlengthsandconsensussequencesofthevariablepartsoftherepeats[1,6].Veryrecently,wefoundthatafamilyofninesmallproteoglycans,formingthreedistinctsubfam-ilies: classIcontainsbiglycan/PG-Ianddecorin/PG-II;classII-lumican,ﬁbromodulin,PRELP,keratocan,andosteoadherin,andclassIII-epiphycan/PG-Lbandosteoglycin/osteoinductivefactorhavesuper-repeatsofLRRs. Weproposedanevolutionaryhistoryofthesesmallproteoglycans[5].Comparativeanalysisof34availableproteinsequencesrevealedthattheseproteoglycanshavetwotypesofLRRs,whichwecallS andT.ThetypeS LRRis21residueslongandhastheconsensussequenceofxxaPzxLPxxLxxLxLxxNxI.ThetypeT LRRhas26residues;itsconsensussequenceiszzxxaxxxxFxxaxxLxxLxLxxNxL.Inboth,“x”indicatesvariableresidue;“z”isfrequentlyagap;“a”isVal,Leu,orIle;and“I”and“L”isIleorLeu. ThesetypeS andT LRRsareorderedintotwosuper-motifs-STT withabout73residuesinclassesIandIIandST withabout47residuesinclassIII.ThetwelveLRRsinthesmallproteoglycansofIandIIarebestrepresentedas(STT)
Modulation of Endothelial Cell Adhesion by Hevin, an Acidic Protein Associated with High Endothelial Venules (1996)

High endothelial venules (HEV) are specialized plump postcapillary venules in lymphoid tissues that support high levels of lymphocyte extravasation from the blood. We have recently identified a novel human transcript, expressed to high levels in HEV, that encodes a secreted, acidic protein closely related to the anti-adhesive extracellular matrix protein known as BM-40, osteonectin, and SPARC (secreted protein acidic and rich in cysteine). Here, we show that this protein, designated hevin, is associated with basal, lateral, and apical surfaces of HEV cells, and unlike MECA-79 antigen, is not expressed on the underlying basement membrane. In contrast to fibronectin or other adhesive extracellular matrix proteins, purified hevin does not support endothelial cell adhesion in vitro. Moreover, addition of soluble exogenous hevin inhibits attachment and spreading of endothelial cells on fibronectin substrates. Hevin-treated cells do not form focal adhesions and exhibit a rounded morphology. Together, these results suggest that hevin is an abundant extracellular protein that modulates high endothelial cell adhesion to the basement membrane.
The effect of severe zinc deficiency on the morphology of the rat retinal pigment epithelium. (1982)

Male Sprague-Dawley weanling rats maintained on a controlled dietary zinc intake had an accumulation of osmiophilic inclusion bodies in the retinal pigment epithelium (RPE) of the zinc-deficient group. At 7 weeks of zinc deficiency there were marked ultrastructural alterations of the RPE. In some instances a deepening of the basal infoldings of the cells of the RPE were observed. There was also vesiculation and degeneration of the photoreceptor outer segments. No changes were observed in the pair-fed, weight-restricted, and ad libitum-fed controls. The possible functions of zinc in the retina are discussed.
Evaluation of the In Vitro Pyrogen Test System Based on Proinflammatory Cytokine Release from Human Monocytes: Comparison with a Human Whole Blood Culture Test System and with the Rabbit Pyrogen Test (2002)

The reliability of an in vitro pyrogen test system based on proinflammatory cytokine release from human monocytic cells was assessed by comparison with a test system based on a human whole blood culture as well as with the conventional rabbit pyrogen test. The human cells used as the pyrogen indicator cells were newly selected by subcloning of a human monocytic cell line, Mono-Mac-6. The selected cells, named MM6-CA8, responded to various pyrogens, including endotoxin, peptidoglycan (PG), Staphylococcus aureus Cowan 1 (SAC), and poly(I x C), with a high sensitivity and produced proinflammatory cytokines, such as interleukin 1 (IL-1), IL-6, and tumor necrosis factor alpha. Among these cytokines, IL-6 was produced most sensitively in response to traces of the pyrogens and detected in the largest quantities in the culture medium. The cytokine-producing responses of MM6-CA8 cells correlated significantly with the responses of cultured human whole blood, which represents an ex vivo culture test system reproducing pyrogen-induced cytokine production in the human body. In terms of cytokine inducibility, the pyrogens were ranked in the order endotoxin > PG > poly (I. C) > SAC in both culture systems, a ranking which almost agreed with the ranking of their pyrogenicity as assessed by the rabbit pyrogen test. These results suggest that the in vitro responsiveness of MM6-CA8 cells to various pyrogens is highly relevant for human pyrogenic reactions. Therefore, the in vitro test system is useful and reliable for detecting the presence of materials that are pyrogenic for humans.
Inhibition of T cell activation by a monoclonal antibody reactive against the alpha 3 domain of human MHC class I molecules. (1994)

A long term goal of investigators working in our laboratory has been to develop new mAbs for use as immunosuppressive agents. As a means toward achieving this goal, several new mAbs (hybridomas) have been developed by screening fusions for supernatants that possess T cell-inhibitory properties. Of these new mAbs, one mAb, designated 5H7, has been shown to possess both a unique combination of specificity for a monomorphic determinant of the alpha 3 domain of human class I MHC heavy chains and highly potent T cell inhibitory properties. mAb 5H7 profoundly inhibited T cell proliferation in response to anti-CD3 mAb in primary or secondary allogenic MLR or in primary human anti-mouse xenogenic MLR. mAb 5H7 inhibited expression of an early T cell activation marker, Leu23 (CD69); expression of IL-2Rs; and IL-2 production by both CD4+ and CD8+ T cells. mAb 5H7 inhibited IL-2 release by the Jurkat (E6-1) human T cell leukemia line in response to immobilized anti-CD3 mAb, thus, providing further evidence that 5H7 can inhibit activation directly at the level of the T cell. 5H7 profoundly blocked CD3-dependent (anti-CD3, anti-CD3 plus PMA, or anti-CD3 plus anti-CD28) pathways, but only partially blocked a CD3-independent (anti-CD28 plus PMA) pathway of T cell activation. In conclusion, class I MHC molecules that are expressed on the T cell may regulate early TCR/CD3-dependent signaling events. In addition, 5H7 mAb may provide a reagent for suppression of cellular immunity in vivo.
Nature and Patterns of Proteins during Cotton Seed Development (1979)

Patterns of accumulation and ontogenetic relationships among proteins of cotton (Gossypium hirsutum L.) seeds were examined between 10 days postanthesis and maturity (56 days). Total and extractable nitrogen contents were determined; alkali- and water-soluble proteins were assayed quantitatively and electrophoretically. Two alkali-soluble proteins present in the electrophoretogram of mature embryos first appeared at 21 days postanthesis; most of the final profile was established by 28 days. Except for minor changes centering around the 7th week of development, the pattern from 28 days to maturity was marked by intensification of bands. The quantity of water-soluble nitrogen increased through the first 21 days of development, then declined until 42 days, when it again began to increase; it reached its highest level at maturity. There was evidence of a high peptide content 7 weeks postanthesis.
Expression Profile of MicroRNAs in Serum: A Fingerprint for Esophageal Squamous Cell Carcinoma (2010)

This panel of 7 serum miRNAs holds promise as a novel blood-based biomarker for the diagnosis of ESCC.
Production of in vitro amplified DNA pseudolibraries and high-throughput cDNA target amplification (2007)

The overall efficiency of the simple protocol collection approaches 100% for targets from libraries with low complexity such as Drosophila and yields >80% of amplicons up to 3 kb size in the case of human cDNA.
The Impact of Glu102Lys on the Factor X Function in a Patient with a Doubly Homozygous Factor X Deficiency (Gla14Lys and Glu102Lys) (2000)

Two homozygous point mutations were found in a patient with factor X (FX) deficiency; One results in substitution of Lys for Gla+ 14 and the second causes a Lys substitution for Glu102. The proposita has a severely reduced FX coagulant activity in the extrinsic (<1% of normal) and in the intrinsic (30% of normal) system of coagulation and after activation with Russel's viper venom (18% of normal). The FX antigen is reduced in this patient to 20% of normal. The substitution of Lys for Glu102 in FX deficiency has been reported previously in a heterozygous state in conjunction with a Lys for Gla+14 substitution and with a Pro for Ser334 substitution. The contribution of the Lys for Glu102 substitution in the observed combined FX defect in these patients was unclear. The mutation causing the Glu102Lys substitution was introduced by site directed mutagenesis into a wild-type FX cDNA, and recombinant protein was expressed in HEK 293 cells. Compared to the wild-type FX cDNA, the mutant construct had a 67% activity upon activation in the extrinsic system, 93% activity upon activation in the intrinsic system and 72% after activation with RVV. The data presented show that the substitution of Lys for Glu102 results in a minor functional defect of the FX molecule.
Evaluation of a novel biomaterial in the suprachoroidal space of the rabbit eye. (2002)

POE suprachoroidal injections, an easy, controllable, and reproducible procedure, were well tolerated in the rabbit eye. POE appears to be a promising biomaterial to deliver drugs focally to the choroid and the retina.
Fibrogenesis and fibrosis in inflammatory bowel diseases: Good and bad side of same coin? (2013)

Fibrogenesis in inflammatory bowel diseases is a complex phenomenon aimed at mucosal repair. However, it may provoke intestinal fibrosis with the development of strictures which require surgery. Therefore, fibrogenesis may be considered as a "two-faced" process when related to chronic intestinal inflammation. Many types of cells may be converted into the fibrogenic phenotype at different levels of the intestinal wall. A complex interaction of cytokines, adhesion molecules and growth factors is involved in the process. We report an overview of recent advances in molecular mechanisms of stricturizing Crohn's disease (CD) including the potential role of trasforming growth factor beta, protein kinase C and Ras, Raf and ERK proteins. Fibrotic growth factors such as vascular endothelial growth factor and platelet-derived growth factor, as well as the Endothelial-to-Mesenchymal Transition induced by transforming growth factor-β, are considered. Finally, our experience, focused on tumor necrosis factor α (the main cytokine of inflammatory bowel diseases) and the link between syndecan 1 (a heparan sulphate adhesion molecule) and basic fibroblast growth factor (a strong stimulator of collagen synthesis) is described. We hypothesize a possible molecular pattern for mucosal healing as well as how its deregulation could be involved in fibrotic complications of CD. A final clinical point is the importance of performing an accurate evaluation of the presence of fibrotic strictures before starting anti-tumor necrosis α treatment, which could worsen the lesions.
Regeneration of peripheral nerve after transplantation of CD133+ cells derived from human peripheral blood (2008)

The results show that CD133(+) cells have potential for enhancement of histological and functional recovery from peripheral nerve injury. This attractive cell source could be purified easily from peripheral blood and could be a feasible autologous candidate for peripheral nerve injuries in the clinical setting.