gebhart/patrepeval huggingface dataset:
Bottom-Up Synthesis of Graphene Monolayers with Tunable Crystallinity and Porosity (2019)

We present a method for a bottom-up synthesis of atomically thin graphene sheets with tunable crystallinity and porosity using aromatic self-assembled monolayers (SAMs) as molecular precursors. To this end, we employ SAMs with pyridine and pyrrole constituents on polycrystalline copper foils and convert them initially into molecular nanosheets-carbon nanomembranes (CNMs)- via low-energy electron irradiation induced cross-linking and then into graphene monolayers via pyrolysis. As the nitrogen atoms are leaving the nanosheets during pyrolysis, nanopores are generated in the formed single-layer graphene. We elucidate the structural changes upon the cross-linking and pyrolysis down to the atomic scale by complementary spectroscopy and microscopy techniques including X-ray photoelectron and Raman spectroscopy, low energy electron diffraction, atomic force, helium ion, and high-resolution transmission electron microscopy, and electrical transport measurements. We demonstrate that the crystallinity and porosity of the formed graphene can be adjusted via the choice of molecular precursors and pyrolysis temperature, and we present a kinetic growth model quantitatively describing the conversion of molecular CNMs into graphene. The synthesized nanoporous graphene monolayers resemble a percolated network of graphene nanoribbons with a high charge carrier mobility (∼600 cm<sup>2</sup>/(V s)), making them attractive for implementations in electronic field-effect devices.
Universal Solid-Phase Approach for the Immobilization, Derivatization, and Resin-to-Resin Transfer Reactions of Boronic Acids (2001)

Boronic acid-containing molecules are employed in a broad range of biological, medicinal, and synthetic applications. These compounds, however, tend to be difficult to handle by solution-phase methods. Herein, this problem is addressed with the development of the first general solid-phase approach for the derivatization of functionalized boronic acids. This approach is based on the use of a diethanolamine resin anchor that facilitates boronic acid immobilization by avoiding the need for exhaustive removal of water in the esterification process. The immobilization of a wide variety of boronic acids onto N,N-diethanolaminomethyl polystyrene (DEAM-PS, 1) can be performed within minutes by simple stirring in anhydrous solvents at room temperature. Evidence for the formation of a bicyclic diethanolamine boronate with putative N-B coordination was shown by (1)H NMR analysis of DEAM-PS-supported p-tolylboronic acid. The hydrolytic cleavage of the same model boronic acid from the DEAM-PS resin was studied by UV spectroscopy. Hydrolysis and attachment were shown to occur under a rapidly attained equilibrium, and a large excess of water (>32 equiv) is required to effect a practically quantitative release of boronic acids from DEAM-PS. Despite their relative sensitivity to water and alcohols, DEAM-PS-bound arylboronic acids functionalized with a formyl, a bromomethyl, a carboxyl, or an amino group can be transformed in good to excellent yields into a wide variety of amines, amides, anilides, and ureas, respectively. Ugi multicomponent reactions on DEAM-PS-supported aminobenzeneboronic acids, derivatization of multifunctional arylboronic acids, and sequential reactions can also be carried out efficiently. These new DEAM-PS-supported arylboronic acids can be employed directly into resin-to-resin transfer reactions (RRTR). This type of multiresin process helps eliminate time-consuming cleavage and transfer operations, thereby considerably simplifying the outlook of combinatorial library synthesis by manual or automated means. This concept was illustrated by a set of optimized procedures for the Suzuki cross-coupling and the borono-Mannich reactions.
Caffeic acid phenethyl ester to inhibit posterior capsule opacification in rabbits (1997)

These preliminary results indicate that CAPE is effective in suppressing PCO in pigmented rabbits and may be beneficial in clinical use in humans because it has no documented harmful effects on normal cells.
cis-acting sequences involved in human immunodeficiency virus type 1 RNA packaging (1995)

We have previously described a series of human immunodeficiency virus type 1-based vectors in which efficient RNA encapsidation appeared to correlate with the presence of a 1.1-kb env gene fragment encompassing the Rev-responsive element (RRE). In this report, we explore in detail the role of the RRE and flanking env sequences in vector expression and RNA encapsidation. The analysis of a new series of vectors containing deletions within the env fragment failed to identify a discrete packaging signal, although the loss of certain sequences reduced packaging efficiency three- to fourfold. Complete removal of the env fragment resulted in a 100-fold decrease in the vector transduction titer but did not abolish RNA encapsidation. We conclude that the RRE and 3' env sequences are not essential for human immunodeficiency virus type 1 vector encapsidation but may be important in vectors in which a heterologous gene has been placed adjacent to the 5' packaging signal, potentially disrupting its structure.
Sketch-to-collage (2007)

Using query-by-sketch we propose an application to efficiently create collages from image collections. Using rough color strokes that represent the target collage, images are automatically retrieved from a database and segmented to synthesize a new image. The database is indexed using simple geometrical and color features for each region, and histograms that represent these features for each image. The image collection is queried by means of rough strokes on a simple paint tool. The individual segments retrieved are added to the collage using Poisson image editing and alpha matting.
Organ erythrocyte and plasma volumes of tumor-bearing mice; the oligemia of neoplasms. (1951)

Direct determinations were made of the cell and plasma volumes of organs and tumors; on this basis, the organ and average body hematocrits were calculated. Each organ has a characteristic hematocrit with values diminishing in the following order: spleen, liver and lung, kidney.

The blood volume of all tumors examined was much below that of these organs. Experiments indicate that this oligemia of tumors is real and not due to sluggish circulation.
The spliceosome: the most complex macromolecular machine in the cell? (2003)

The primary transcripts, pre-mRNAs, of almost all protein-coding genes in higher eukaryotes contain multiple non-coding intervening sequences, introns, which must be precisely removed to yield translatable mRNAs. The process of intron excision, splicing, takes place in a massive ribonucleoprotein complex known as the spliceosome. Extensive studies, both genetic and biochemical, in a variety of systems have revealed that essential components of the spliceosome include five small RNAs-U1, U2, U4, U5 and U6, each of which functions as a RNA, protein complex called an snRNP (small nuclear ribonucleoprotein). In addition to snRNPs, splicing requires many non-snRNP protein factors, the exact nature and number of which has been unclear. Technical advances, including new affinity purification methods and improved mass spectrometry techniques, coupled with the completion of many genome sequences, have now permitted a number of proteomic analyses of purified spliceosomes. These studies, recently reviewed by Jurica and Moore,1 reveal that the spliceosome is composed of as many as 300 distinct proteins and five RNAs, making it among the most complex macromolecular machines known.
Demodexquantification methods: limitations of confocal laser scanning microscopy (2013)

Funding sources: None. Conflicts of interest: None declared. Madam, We read with interest the recent paper by Sattler et al.1 describing the quantification of Demodex mites using confocal laser scanning microscopy (CLSM). Their work is interesting but we feel that there are limitations to the use of this method for accurately detecting absolute numbers of mites in human skin. Because the role of Demodex in normal or diseased skin is unknown,2 and because of their possible role in modulation of immune reactivity of the follicle3 and an association between the degree of mite infestation and the development of rosacea,4 5 6 the need for accurate reproducible in vivo methods of quantifying mites is becoming increasingly important. Demodex folliculorum and Demodex brevis are most numerous in the sebaceous follicles of the central facial skin of humans. The upper portion and infundibulum of the sebaceous follicle appear to be populated almost entirely by mature adult D. folliculorum (some of which are dead). Histological sections of skin show that mites are orientated with their cephalic portion downwards in the follicular canal and their vermiform opisthosoma upwards protruding into the follicular ostium. Figure 1 in the publication by Sattler et al. nicely shows the opisthosoma of several mites within the infundibulum of a follicle. Figure 2 in their article is unclear, as the ‘lengthy cone‐shaped body’ of Demodex ‘cut sideways’ is not apparent to these authors.
Dynamic Behavior of the Water Droplet Impact on a Textured Hydrophobic/Superhydrophobic Surface: The Effect of the Remaining Liquid Film Arising on the Pillars' Tops on the Contact Time (2010)

We have fabricated a series of textured silicon surfaces decorated by square arrays of pillars whose radius and pitch can be adjusted independently. These surfaces possessed a hydrophobic/superhydrophobic property after silanization. The dynamic behavior of water droplets impacting these structured surfaces was examined using a high-speed camera. Experimental results validated that the remaining liquid film on the pillars' tops gave rise to a wet surface instead of a dry surface as the water droplet began to recede away from the textured surfaces. Also, experimental results demonstrated that the difference in the contact time was subjected to the solid fraction referred to as the ratio of the actual area contacting with the liquid to its projected area on the textured surface. Because the mechanism by which the residual liquid film emerges on the pillars' tops can essentially be ascribed to the pinch-off of the liquid threads, we further addressed the changes in the contact time in terms of the characteristic time of pinch-off of an imaginary liquid cylinder whose radius is related to the solid fraction and the maximum contact area. The match of the theoretical analysis and the experimental results substantiates the assumption aforementioned.
Kulitta: A Framework for Automated Music Composition (2014)

Kulitta is a Haskell-based, modular framework for automated composition and machine learning. A central idea to Kulitta's approach is the notion of abstraction: the idea that something can be described at many different levels of detail. Music has many levels of abstraction, ranging from the sound we hear to a paper score and large-scale structural patterns. Music is also very multidimensional and prone to tractability problems. Kulitta works at many of levels of abstraction in stages as a way to mitigate these inherent complexity problems. Abstract musical structure is generated by using a new category of grammars called probabilistic temporal graph grammars (PTGGs), which are a type of parameterized, context-free grammar that includes variable instantiation, a feature usually only found in grammars for programming languages. This abstract structure can be turned into full music through the use of constraint satisfaction algorithms and equivalence relations based on music theoretic concepts. An extension to an existing algorithm for learning PCFGs provides a way to learn production probabilities for these grammars using corpora of existing music. Kulitta's modules for these features are able to be combined in different ways to support multiple styles of music. Kulitta's important contributions include (1) algorithms and a generalized Haskell implementation to support PTGGs, (2) additional formalization of existing musical equivalence relations along with a new equivalence relation for modeling jazz harmony, (3) an empirical evaluation strategy for measuring the performance of automated composition algorithms, and (4) the extension of a machine-learning algorithm for PCFGs to support a much broader category of grammars (inclusive of PTGGs) via the use of an oracle. Kulitta's musical performance is also promising, demonstrating both stylistic versatility and aesthetically pleasing results.
Differential vesicular distribution and trafficking of MMP‐2, MMP‐9, and their inhibitors in astrocytes (2009)

Astrocytes play an active role in the central nervous system and are critically involved in astrogliosis, a homotypic response of these cells to disease, injury, and associated neuroinflammation. Among the numerous molecules involved in these processes are the matrix metalloproteinases (MMPs), a family of zinc-dependent endopeptidases, secreted or membrane-bound, that regulate by proteolytic cleavage the extracellular matrix, cytokines, chemokines, cell adhesion molecules, and plasma membrane receptors. MMP activity is tightly regulated by the tissue inhibitors of MMPs (TIMPs), a family of secreted multifunctional proteins. Astrogliosis in vivo and astrocyte reactivity induced in vitro by proinflammatory cues are associated with modulation of expression and/or activity of members of the MMP/TIMP system. However, nothing is known concerning the intracellular distribution and secretory pathways of MMPs and TIMPs in astrocytes. Using a combination of cell biology, biochemistry, fluorescence and electron microscopy approaches, we investigated in cultured reactive astrocytes the intracellular distribution, transport, and secretion of MMP-2, MMP-9, TIMP-1, and TIMP-2. MMP-2 and MMP-9 demonstrate nuclear localization, differential intracellular vesicular distribution relative to the myosin V and kinesin molecular motors, and LAMP-2-labeled lysosomal compartment, and we show vesicular secretion for MMP-2, MMP-9, and their inhibitors. Our results suggest that these proteinases and their inhibitors use different pathways for trafficking and secretion for distinct astrocytic functions.
Levitation Forces, Relaxation and Magnetic Stiffness of Melt-Quenched YBa2Cu3Ox (1990)

Measurements of levitation forces on melt-quenched and free sintered YBa 2 Cu 3 O x superconductors show that melt-quenched samples produce forces from 96-170% higher than sintered specimens. The force increases are correlated with higher magnetization values for the melt-quenched material. Similar increases in the magnetic stiffness were also measured. Vertical levitation force relaxation showed less than 5% decrease in one hour. These results have important favorable implications for application to superconducting bearings.
Constitutively Activated Stat3 Induces Tumorigenesis and Enhances Cell Motility of Prostate Epithelial Cells through Integrin β6 (2007)

The persistent activation of signal transducer and activator of transcription 3 (Stat3) is a common feature of prostate cancer. However, little is known about the Stat3 targets that may mediate prostate tumorigenesis. The introduction of an activating mutant form of Stat3 (Stat3-C) into immortalized prostate epithelial cells resulted in tumorigenesis. Stat3-C-expressing cells had decreased E-cadherin levels, increased numbers of lamellipodia and stress fibers, and enhanced migratory capacities compared to vector control-expressing cells, with a concomitant increase in the expression of integrin beta6 and its ligand, fibronectin (FN). Exogenously added FN increased cellular migration, with a concomitant loss of E-cadherin expression. The blockade of integrin alphavbeta6 in Stat3-C-expressing cells inhibited migration, increased E-cadherin levels, and reduced colony formation in soft agar. These results demonstrate the sufficiency of constitutively activated Stat3 in mediating prostate tumorigenesis and identify novel Stat3 targets that are involved in promoting cell migration and transformation.
Structural and functional epitopes of the human adhesion receptor CD58 (LFA‐3) (1992)

CD58 (LFA-3), a heavily glycosylated protein of 40-70 kDa, is expressed on a broad range of hematopoietic and non-hematopoietic cells. It serves as a physiological ligand of the CD2 receptor, present on T cells and natural killer cells, and plays, thus, an important role in lymphocyte adhesion and T cell activation through CD2. Whereas several epitopes and their respective function are known for CD2, a similarly detailed characterization of CD58 is still lacking. We raised a panel of novel murine monoclonal antibodies (mAb) against recombinant human CD58 and describe here the identification of six structurally and/or functionally distinct epitopes on the CD58 molecule. All epitopes were found to be present in equal numbers on a wide range of CD58+ cells, none of them being differentially up-regulated following cell activation or malignant transformation. Two of these epitopes represent functionally relevant sites, involved in binding of CD58 to CD2 and T cell activation via CD2. One further epitope appears to be selectively involved in CD58-mediated activation, whereas the other three displayed no functional effects. The new mAb allow for the first time the detection of CD58 in enzyme-linked immunosorbent assays and immunofluorescence while bound to its receptor CD2 in human serum or on freshly isolated blood cells. Finally, one mAb was found to specifically cross-react with T11TS, the equivalent of CD58 in sheep.
<p>Dynamic Interplay Between Microbiota and Mucosal Immunity in Early Shaping of Asthma and its Implication for the COVID-19 Pandemic</p> (2020)

The crosstalk between host immunity and the external environment in the mucous membranes of the gastrointestinal and respiratory tracts in bronchial asthma has recently been scrutinized. There is compelling evidence that the microbiota at these sites may play an important role in the pathogenesis of this chronic airway disease. The appearance of bacteria early in life in the gut before dissemination to the airways plays a pivotal role in shaping mucosal immunity. Loss of microbial diversity or dysbiosis can result in aberrant immune-mediated inflammation and mucosal barrier disruption, which coincides clinically with the successive development of the "allergic march" in asthma. Microbial manipulation may be effective in curbing asthma development by indirectly preserving homeostatic epithelial barrier functions. The protective effects and mechanisms of immunity-microbiome crosstalk at mucosal sites require further investigation to identify therapeutic and preventive measures in asthma. This topical review aims to highlight new evidence that compromised epithelial barrier function, which results in deregulated crosstalk between the microbiome and host mucosal immune system, is an important disease mechanism in asthma. In the light of current COVID-19 pandemic, the collective findings on the impact of mucosal microbiota on the suceptibility to SARS-CoV-2 infection and severity of COVID-19 is explored. The possible therapeutic implications to target these abnormalities are further discussed.
In situ target-less calibration of turbid media (2017)

The color of an object imaged in a turbid medium varies with distance and medium properties, deeming color an unstable source of information. Assuming 3D scene structure has become relatively easy to estimate, the main challenge in color recovery is calibrating medium properties in situ, at the time of acquisition. Existing attenuation calibration methods use either color charts, external hardware, or multiple images of an object. Here we show none of these is needed for calibration. We suggest a method for estimating the medium properties (both attenuation and scattering) using only images of backscattered light from the system's light sources. This is advantageous in turbid media where the object signal is noisy, and also alleviates the need for correspondence matching, which can be difficult in high turbidity. We demonstrate the advantages of our method through simulations and in a real-life experiment at sea.
Why the enteric nervous system is important to clinicians (2000)

The enteric nervous system (ENS) is central to normal gut function and is involved in most, if not all, disorders of the luminal gastrointestinal tract. The primary pathology of oesophageal and gastrointestinal disorders can lie in the ENS , in adjacent structures such as enteric smooth muscle and gut epithelium, or in extrinsic nerves (local, spinal, and cerebral) controlling gut function. Even if the primary pathology lies in another part of the gut, such as in the mucosa, or outside the gastrointestinal tract, such as in the extrinsic neural pathways, the ENS still serves as the effector neural controller, leading to a disturbance in gut function and generation of symptoms.

The ENS, therefore, serves as a useful therapeutic target for disorders in which it is the source of dysfunction and also for disorders in which it is the effector organ. For example, in treating distal ulcerative colitis, enemas containing the neurally active membrane stabiliser lignocaine have been shown to be effective, suggesting possible involvement of neural processes in the inflammatory process. In patients with irritable bowel syndrome and diarrhoea, there is substantial evidence that the primary disorder is one of cerebral regulation of gut function, mediated …
Computer-Assisted Fluoroscopy-Based Reduction of Femoral Fractures and Antetorsion Correction (2000)

Objective: Intra-operative fluoroscopy is a valuable tool for visualizing underlying bone, implant, and surgical tool positions in orthopedics. It has brought about the minimally invasive surgical technique of intramedullar nailing to fix femoral shaft fractures. However, the limited field of view and two-dimensional property of fluoroscopic images aggravate intra-operative control of surgical parameters. The purpose of this article is to introduce a surgical navigation System based on fluoroscopy that provides missing information for the procedure of femoral fracture fixation.Materials and Methods: Optoelectronic markers are placed on a surgical drill, involved bone fragments, the femoral nail, and the fluoroscope to track their positions. Projection properties of the fluoroscope are acquired through an initial precalibration. The relative positions of bone fragments, implants, and surgical tools are displayed superimposed simultaneously and in real time on multi-planar intra-operative fluoroscopic images. This is achieved by computer simulation of X-ray projections that have taken place with acquisition of the fluoroscopic images. in addition, a method has been developed that allows contactless measurement of three-dimensional anatomic landmarks, based on their representation in fluoroscopic images. in combination with optoelectronic tracking, this enables dynamic calculacion of important surgical parameters such as femoral antetorsion.Results: A pilot surgery showed that fracture reduction can benefit from the developed computer-assisted method. An in-vitro study on computer-assisted measurement of femoral antetorsion demonstrated the high degree of precision of this technique.
The Proapoptotic Molecule BLID Interacts with Bcl-XL and Its Downregulation in Breast Cancer Correlates with Poor Disease-Free and Overall Survival (2010)

BLID is a new binding partner of Bcl-X(L) and a significant prognostic factor in breast cancer.