gebhart/patrepeval huggingface dataset:
Ein einfacher lithographischer Ansatz zur Herstellung regelmäßig angeordneter Mulden im Mikrometermaßstab zur Kontrolle des Zellwachstums (1999)

Hydrophobe n-Alkanthiolat-Böden und Wände aus hydrophilen Dreischicht-Poly(acrylsäure)/Poly(ethylenglycol)-Nanocomposit-Polymeren wurden zur Konstruktion von gitterförmig angeordneten Mulden mit Innenabmessungen von 63 μm verwendet. Makrophagenzellen innerhalb dieser Mulden sind nicht in der Lage, über die Muldenwände hinweg zu wachsen (siehe Bild).
On the sorting-complexity of suffix tree construction (2000)

The suffix tree of a string is the fundamental data structure of combinatorial pattern matching. We present a recursive technique for building suffix trees that yields optimal algorithms in different computational models. Sorting is an inherent bottleneck in building suffix trees and our algorithms match the sorting lower bound. Specifically, we present the following results. (1) Weiner [1973], who introduced the data structure, gave an optimal 0 ( n )-time algorithm for building the suffix tree of an n -character string drawn from a constant-size alphabet. In the comparison model, there is a trivial Ο( n log n )-time lower bound based on sorting, and Weiner's algorithm matches this bound. For integer alphabets, the fastest known algorithm is the O ( n log n )time comparison-based algorithm, but no super-linear lower bound is known. Closing this gap is the main open question in stringology. We settle this open problem by giving a linear time reduction to sorting for building suffix trees. Since sorting is a lower-bound for building suffix trees, this algorithm is time-optimal in every alphabet mode. In particular, for an alphabet consisting of integers in a polynomial range we get the first known linear-time algorithm. (2) All previously known algorithms for building suffix trees exhibit a marked absence of locality of reference, and thus they tend to elicit many page faults (I/Os) when indexing very long strings. They are therefore unsuitable for building suffix trees in secondary storage devices, where I/Os dominate the overall computational cost. We give a linear-I/O reduction to sorting for suffix tree construction. Since sorting is a trivial I/O-lower bound for building suffix trees, our algorithm is I/O-optimal.
Novel Therapeutic Strategy for Restenosis Using Ribozyme Oligonucleotides Against Transforming Growth Factor-β (2000)

P197 Background Since the mechanisms of atherosclerosis or restenosis after angioplasty have been postulated to involve an increase in TGF-β, a selective decrease in TGF-βmay have therapeutic value. Thus, we employed the ribozyme a unique class of RNA molecules that not only store information but also process catalytic activity, to selectively inhibit TGF-βexpression. Methods & Results We constructed ribozyme oligonucleotides targeted to the sequence of TGF-βgene which shows 100 % homology among human, rat and mouse. The specificity of ribozyme against TGF-βgene was confirmed by selective inhibition of TGF-βmRNA in cultured human VSMC as well as balloon-injured blood vessels in vivo. In vitro study Transfection of TGF-βribozyme ON into human VSMC by cationic liposome significantly decreased mRNA expression and protein of TGF-βinduced by Ang II as compared to control In vivo study Transfection of FITC-labeled ribozyme ON resulted in fluorescence in the balloon-injured vessels at 1 day after transfection. The fluorescence was localized primarily in cell nuclei , and persisted for up to 2 weeks after transfection.And then,transfection of TGF-βribozyme ON into rat cartid balloon injry model significantly decreased mRNA expression of TGF-βinduced by balloon injry ,and have significant inhibitory effects on neointimal formation after vascular injury(P
Recent Studies on the Application of Microwave-Assisted Method for the Preparation of Heterogeneous Catalysts and Catalytic Hydrogenation Processes (2023)

Currently, microwave radiation is widely used in various chemical processes in order to intensify them and carry out processes within the framework of "green" chemistry approaches. In the last 10 years, there has been a significant increase in the number of scientific publications on the application of microwaves in catalytic reactions and synthesis of nanomaterials. It is known that heterogeneous catalysts obtained under microwave activation conditions have many advantages, such as improved catalytic characteristics and stability, and the synthesis of nanomaterials is accelerated several times compared to traditional methods used to produce catalysts. The present review article is to summarize the results of modern research on the use of microwave radiation for the synthesis of heterogeneous catalytic nanomaterials and discusses the prospects for research in the field of microwave-induced liquid-phase heterogeneous catalysis in hydrogenation.
A gaze-preserving group video conference system using screen-embedded cameras (2017)

In this paper, we propose a system that presents correct gaze directions of each user in a group-to-group video conference. It is known that gaze direction plays a significant role in face-to-face communication. However, in ordinary video conference systems, there is a problem that gaze directions cannot be correctly transmitted to a user in the other side since the camera is placed on the top or bottom of the display. We propose a method to generate images of each person from an appropriate viewpoint position using Kinect and screen-embedded cameras and to present the images to the user. By estimating each user's gaze direction and rendering the image of the person who the user is looking at from the users' viewpoint position, it is possible to present an image suitable for each user even in a group-to-group situation. We show demonstration of a group-to-group video conference using the proposed system and show that the system can present images suitable for each user.
Sparse Scanning Electron Microscopy for Imaging and Segmentation in Connectomics (2018)

Sparse Scanning Electron Microscopy can be used in combination with Inpainting algorithms to reduce acquisition time and electron dose. Especially for three-dimensional (3D) or very large field of view imaging, acquisition time reductions are of large importance to the community. Dose reduction is of importance in imaging material that is sensitive to electron radiation. In this study we demonstrate a workflow that acquires data by performing a sparse scan at random positions on a specimen. The sparse data is reconstructed to a full grid image by a GPU accelerated dictionary based inpainting algorithm. The reconstructed data is suitable to be used for automatic semantic segmentation of neuron structures. We demonstrate the procedure on two key segmentation applications in connectomics (cell membranes and mitochondria) and show that the overall segmentation quality improves notably compared to data from a conventional raster scan acquired with the same total dose per image. Alternatively, the total dwell time per pixel can be reduced by 33% while maintaining the same level of quality of the segmentation. These results demonstrate that sparse scanning and reconstruction can increase the effective data acquisition rates without sacrificing on quality for the end user segmentation application.
Magnetic order or charge-density wave inLa2NiO4by Mössbauer spectroscopy (1984)

Measurements of M\"ossbauer absorption spectra of $^{57}\mathrm{Fe}$: ${\mathrm{La}}_{2}$Ni${\mathrm{O}}_{4}$ at 297, 77, and 4.2 K provide evidence, at the lowest temperatures, of magnetic order in a sample containing $^{57}\mathrm{Fe}^{3+}$-ion impurities and some ${\mathrm{La}}_{2+n}{\mathrm{Ni}}_{1+n}{\mathrm{O}}_{4+3n}$ intergrowth. M\"ossbauer emission spectra of $^{57}\mathrm{Co}$: ${\mathrm{La}}^{2}$Ni${\mathrm{O}}_{4}$ at 77 and 4.2 K show magnetic order coexisting with paramagnetism in a sample containing a small concentration of $^{57}\mathrm{Co}$-ion impurities and some ${\mathrm{La}}_{2+n}{\mathrm{Ni}}_{1+n}{\mathrm{O}}_{4+3n}$ intergrowth. These results are interpreted as evidence for competition between magnetic ordering and charge-density-wave formation among electrons of a narrow ${\ensuremath{\sigma}}_{{x}^{2}\ensuremath{-}{y}^{2}}^{*}$ band; intergrowths, impurities, and nonstoichiometry favor magnetic ordering.
Pharmacology of Antagonists of Angiotensin I and II (1972)

The octapeptide analogues 8-Cys-AII, 8-Ile-AII, 4-Phe-8-Tyr-AII, and p -fluoro-4-Phe-AII were potent competitive antagonists of angiotensin I and II (AI and AII) in rat uterus strips, whereas the decapeptide analogues 4-Phe-8-Tyr-AI and 8-Ile-AI were weak antagonists, 8-Cys-AII and 8-Ile-AII were potent antagonists of the rise in blood pressure induced by angiotensin, although 4-Phe-8-Tyr-AII and p -fluoro-4-Phe-AII were less potent antagonists. AI was rapidly converted and was equipotent to AII in vivo, but 8-Ile-AI was a hundred times less potent than 8-Ile-AII. However, some conversion of 8-Ile-AI did occur, since SQ 20881 (an inhibitor of angiotensin-converting enzyme) markedly diminished the All antagonistic action of 8-Ile-AI. The decapeptides AI, 8-Ile-AI, and 4-Phe-8-Tyr-AI were potent competitive antagonists of the hydrolysis of hippurylhistidylleucine by converting enzyme in vitro. Infusion of the octapeptide and the decapeptide angiotensin analogues resulted in a significant lowering of the blood pressure in anesthetized rats treated with phenoxybenzamine and propranolol and made acutely hypertensive by unclamping a renal pedicle that had been temporarily occluded. The decapeptide analogues, therefore, can function as inhibitors of angiotensin-converting enzyme and simultaneously generate octapeptide antagonists in vivo.
Studies on bacteriophage MS2. VIII. Evidence for dimer formation of MS2 RNA by reaction with formaldehyde at acidic pH (1970)

Abstract Reaction of 27 SMS2 RNA with formaldehyde normally results in an unfolded, 13.4 S form. At acidic pH, however, and under the proper ionic conditions, a compact component sedimenting at 36–40 S was obtained. The molecular weight of this species corresponds to a dinner. The formaldehyde concentration was not critical, and approximately the same number of base pairs had been opened in the compact and in the unfolded form. Presumably dimers, which had been specifically formed under defined conditions, were stabilized by formaldehyde‐induced crosslinks. Similar dimers were formed by 16 S and by 23 S ribosomal RNA, but not by tRNA.
Tissue engineering: state of the art in oral rehabilitation (2009)

More than 85% of the global population requires repair or replacement of a craniofacial structure. These defects range from simple tooth decay to radical oncologic craniofacial resection. Regeneration of oral and craniofacial tissues presents a formidable challenge that requires synthesis of basic science, clinical science and engineering technology. Identification of appropriate scaffolds, cell sources and spatial and temporal signals (the tissue engineering triad) is necessary to optimize development of a single tissue, hybrid organ or interface. Furthermore, combining the understanding of the interactions between molecules of the extracellular matrix and attached cells with an understanding of the gene expression needed to induce differentiation and tissue growth will provide the design basis for translating basic science into rationally developed components of this tissue engineering triad. Dental tissue engineers are interested in regeneration of teeth, oral mucosa, salivary glands, bone and periodontium. Many of these oral structures are hybrid tissues. For example, engineering the periodontium requires growth of alveolar bone, cementum and the periodontal ligament. Recapitulation of biological development of hybrid tissues and interfaces presents a challenge that exceeds that of engineering just a single tissue. Advances made in dental interface engineering will allow these tissues to serve as model systems for engineering other tissues or organs of the body. This review will begin by covering basic tissue engineering principles and strategic design of functional biomaterials. We will then explore the impact of biomaterials design on the status of craniofacial tissue engineering and current challenges and opportunities in dental tissue engineering.
Cardiac uptake of progenitor cells in patients with moderate-to-severe left ventricular failure scheduled for cardiac resynchronization therapy (2006)

Moderate-to-severe chronic CHF is not associated with elevated PC levels in the systemic circulation. A measurable cardiac uptake of CD34(+) and CD34(+)/CD117(+)PC cannot be demonstrated by FACS analysis in this cohort of patients.
Inverting overdetermined Toeplitz systems with application to blind block-adaptive equalization (2002)

Linear channel equalization in block transmission systems amounts to inverting Toeplitz systems of linear equations. Motivated by limitations of a previous blind block equalizer, we derive properties and investigate the class of tall Toeplitz matrix inverses which themselves exhibit (even approximate) Toeplitz structure. The class is characterized by the size of leading and trailing all-zero block submatrices, and interesting links as well as optimal choices of the size parameter are established with the number of minimum-phase zeros of the underlying channel transfer function. Exploiting the properties of such equalizers we derive a direct blind adaptive equalizer and illustrate superiority over competing approaches. It is also shown that the optimum delay for blind block equalization corresponds to the number of maximum-phase channel zeros.
Table S2 from An AIB1 Isoform Alters Enhancer Access and Enables Progression of Early-Stage Triple-Negative Breast Cancer (2023)

&lt;p&gt;A list of enriched pathways using Gene Set Enrichment Analysis (GSEA).&lt;/p&gt;
MTL-CEBPA Combined with Immunotherapy or RFA Enhances Immunological Anti-Tumor Response in Preclinical Models (2021)

The transcription factor CEBPA is a master regulator of liver homeostasis, myeloid cell differentiation and is downregulated in several oncogenic diseases. MTL-CEBPA is a small activating RNA drug which upregulates gene expression of CEBPA for treatment of hepatocellular carcinoma (HCC). We investigate whether MTL-CEBPA has immune modulatory effects by combining MTL-CEBPA with an anti-PD-1 checkpoint inhibitor (CPI) and/or radiofrequency ablation (RFA) in two preclinical models. First, mice with two flanks of HCC tumors (BNL) were treated with combinations of RFA (right flank), anti-PD-1 or MTL-CEBPA. The reduction of the left flank tumors was most pronounced in the group treated with RFA+anti-PD1+MTL-CEBPA and 7/8 animals responded. This was the only group with a significant increase in CD8+ and CD49b+/CD45+ tumor infiltrating lymphocytes (TIL). Second, a combination of anti-PD-1+MTL-CEBPA was tested in a CT26 colon cancer model and this treatment significantly reduced tumor size, modulated the tumor immune microenvironment and increased TILs. These data suggest a clinical role for combination treatment with CPIs, RFA and MTL-CEBPA through synergistic priming of the immune tumor response, enabling RFA and CPIs to have a pronounced anti-tumor effect including activity in non-treated tumors in the case of RFA.
Estrogenic side effects of androgen deprivation therapy. (2007)

Androgen deprivation therapy (ADT) is part of standard therapy for locally advanced or metastatic prostate cancer and is frequently used in men with a rising prostate-specific antigen following radical prostatectomy or radiation therapy. In some men, ADT may be administered for years or even decades. The intended therapeutic effect of ADT is testosterone deficiency. Because estrogen is a normal metabolite of testosterone, ADT also results in estrogen deficiency. ADT has a variety of adverse effects, many of which are primarily related to estrogen deficiency. Bone mineral density may decrease by 4% to 13% per year in men receiving ADT. The fracture rate for patients on ADT averages 5% to 8% per year of therapy. Hot flashes, gynecomastia, and breast tenderness are common side effects associated with ADT. In the clinic, minimum baseline testing should include weight measurement, blood pressure reading, and fasting lipid panel and serum glucose tests. Currently, there are no large outcome trials in men on ADT testing the available therapies for adverse effects. No therapies are specifically approved for treatment of adverse effects in men on ADT. Although some therapies can be used for a single indication (based upon small studies), there is currently no agent to treat the multiple estrogenic side effects of ADT.
A preliminary study investigating the quantification of beat-to-beat in seismocardiogram signals (2013)

Ballistocardiography and seismocardiography are both non-invasive mechanical measurements of the vibrations of the body in response to the heartbeat. The ballistocardiogram (BCG) signal represents the movements of the whole body in response to cardiac ejection of blood into the vasculature; the seismocardiogram (SCG) corresponds to local vibrations of the chest wall associated with sub-audible tissue and blood movement and audio frequency heart-valve closure dynamics. This paper focuses on methods for quantifying "signal consistency"--a quantitative measure of how morphologically similar each heartbeat in a patient's recording is compared to the ensemble average taken over the recording. Before comparing each beat to the average, known physiological sources of inconsistency--such as respiratory amplitude and timing variability--are removed, then the remaining inconsistency is quantified. Previously described methods for BCG signals are expanded to fit the high-frequency (> 20 Hz) components of the SCG. The use of this method in future work could help enable proactive management of heart disease in extra-clinical settings.
Imaging, object detection, and change detection with a polarized multistatic GPR array (2023)

A polarized detection system performs imaging, object detection, and change detection factoring in the orientation of an object relative to the orientation of transceivers. The polarized detection system may operate on one of several modes of operation based on whether the imaging, object detection, or change detection is performed separately for each transceiver orientation. In combined change mode, the polarized detection system performs imaging, object detection, and change detection separately for each transceiver orientation, and then combines changes across polarizations. In combined object mode, the polarized detection system performs imaging and object detection separately for each transceiver orientation, and then combines objects across polarizations and performs change detection on the result. In combined image mode, the polarized detection system performs imaging separately for each transceiver orientation, and then combines images across polarizations and performs object detection followed by change detection on the result.
Structures of engineered Clostridium botulinum neurotoxin derivatives (2011)

Targeted secretion inhibitors (TSIs) are a new class of engineered biopharmaceutical molecules derived from the botulinum neurotoxins (BoNTs). They consist of the metalloprotease light chain (LC) and translocation domain (Hn) of BoNT; they thus lack the native toxicity towards motor neurons but are able to target soluble N-ethylmaleimide-sensitive fusion protein attachment receptor (SNARE) proteins. These functional fragment (LHn) derivatives are expressed as single-chain proteins and require post-translational activation into di-chain molecules for function. A range of BoNT derivatives have been produced to demonstrate the successful use of engineered SNARE substrate peptides at the LC-Hn interface that gives these molecules self-activating capabilities. Alternatively, recognition sites for specific exoproteases can be engineered to allow controlled activation. Here, the crystal structures of three LHn derivatives are reported between 2.7 and 3.0 Å resolution. Two of these molecules are derivatives of serotype A that contain a SNARE peptide. Additionally, a third structure corresponds to LHn serotype B that includes peptide linkers at the exoprotease activation site. In all three cases the added engineered segments could not be modelled owing to disorder. However, these structures highlight the strong interactions holding the LHn fold together despite the inclusion of significant polypeptide sequences at the LC-Hn interface.
Radial shear strain elastography imaging of carotid atherosclerotic plaques in a porcine model (2013)

The objective is to show the feasibility of shear strain elastography (SSE) in vivo with intravascular ultrasound (IVUS) radio-frequency (RF) data acquired at 20 MHz in carotid arteries of atherosclerotic pigs.We previously proposed the Lagrangian speckle model estimator (LSME) to estimate the strain tensor including the shear strain that could be involved in atherosclerotic plaque hemorrhage, inflammation and rupture mechanisms.However, the LSME performance to compute SSE had never been validated.Atherosclerotic pigs with significant plaques on carotids were studied.To induce atherosclerosis, pigs were put on an atherogenic diet and partial ligations of common carotid arteries were performed.Diabetes was induced by selective intra-arterial injection of streptozotocin.IVUS acquisitions were performed before sacrifice and histology analyses were realized on fixed dissected carotids.SSE maps at end diastole were estimated with a new implementation of the LSME and matching with histology sections was realized.SSE clearly identified all plaques with cohabitation of high positive and high negative shear values, and minimum shear elsewhere within the vessel wall.This study demonstrates the performance of the LSME implementation to estimate the shear strain distribution, and the feasibility of SSE to highlight atherosclerotic plaque vulnerability characteristics.
Characterization of blood in an encrustation on an African mask: spectroscopic and direct analysis in real time mass spectrometric identification of haem (2013)

Prior to exhibiting an African Komo mask from the collections of the Detroit Institute of Arts, a multianalytical approach was undertaken to characterize the flaking encrusted coating on the surface of the mask. Preliminary XRF and FTIR examination of the coating on the Komo mask revealed the presence of significant quantities of iron and protein, possibly indicating the presence of blood. Raman spectroscopy showed evidence for the porphyrin structure of haem as well. To confirm that blood was indeed present in the coating, we developed a novel method for identifying the haem moiety from blood by use of in situ methylation and direct analysis in real time mass spectrometry (DART-MS). Following a denaturing step with formic acid, the resulting solution was combined with an excess of phenyltrimethylammonium hydroxide to promote desorption, applied to a melting point tube, and placed into the direct analysis in real time ion source gas stream at 550 °C. The permethylated haem ion (m/z 644.208) from myoglobin, haemoglobin, fresh blood, and blood aged in the laboratory for 10 years was readily observed above the background. By the described DART-TOF-MS method, permethylated haem was positively identified in the mask coating, confirming the presence of blood. This method has obvious utility in forensic science beyond that for identifying blood incorporated in cultural heritage materials.