gebhart/patrepeval huggingface dataset:
Functional Interaction between U1snRNP and Sam68 Insures Proper 3′ End Pre-mRNA Processing during Germ Cell Differentiation (2019)

Male germ cells express the widest repertoire of transcript variants in mammalian tissues. Nevertheless, factors and mechanisms underlying such pronounced diversity are largely unknown. The splicing regulator Sam68 is highly expressed in meiotic cells, and its ablation results in defective spermatogenesis. Herein, we uncover an extensive splicing program operated by Sam68 across meiosis, primarily characterized by alternative last exon (ALE) regulation in genes of functional relevance for spermatogenesis. Lack of Sam68 preferentially causes premature transcript termination at internal polyadenylation sites, a feature observed also upon depletion of the spliceosomal U1snRNP in somatic cells. Notably, Sam68-regulated ALEs are characterized by proximity between U1snRNP and Sam68 binding motifs. We demonstrate a physical association between Sam68 and U1snRNP and show that U1snRNP recruitment to Sam68-regulated ALEs is impaired in Sam68<sup>-/-</sup> germ cells. Thus, our study reveals an unexpected cooperation between Sam68 and U1snRNP that insures proper processing of transcripts essential for male fertility.
Tracking multiple articulated objects using physics engines: Improvement using multi scale decomposition and quadtrees (2010)

This paper presents a new method to accelerate the automatic tracking of multiple articulated objects in video sequences. The tracking method exploits the physics modeling of the articulated objects. The physics approach has numerous advantages such as the capability to let multiple models interact when tracking simultaneously multiple objects. Solving the tracking problem is generally done with an iterative scheme involving the computation of numerous forces, which usually turns out to be time consuming. This paper tackles the computational cost bottleneck by introducing a multi scale decomposition of the force maps. At each step of the tracking optimization scheme the multiple force maps are efficiently combined using a quadtree structure to recover the resulting forces. We demonstrate through multiple experiments that our results are both exact and drastically faster than the standard computation scheme.
Tumor-Infiltrating Myeloid Cells Activate Dll4/Notch/TGF-β Signaling to Drive Malignant Progression (2014)

Myeloid cells that orchestrate malignant progression in the tumor microenvironment offer targets for a generalized strategy to attack solid tumors. Through an analysis of tumor microenvironments, we explored an experimental model of lung cancer that uncovered a network of Dll4/Notch/TGF-β1 signals that links myeloid cells to cancer progression. Myeloid cells attracted to the tumor microenvironment by the tumor-derived cytokines CCL2 and M-CSF expressed increased levels of the Notch ligand Dll4, thereby activating Notch signaling in the tumor cells and amplifying tumor-intrinsic Notch activation. Heightened Dll4/Notch signaling in tumor cells magnified TGF-β-induced pSMAD2/3 signaling and was required to sustain TGF-β-induced tumor cell growth. Conversely, Notch blockade reduced TGF-β signaling and limited lung carcinoma tumor progression. Corroborating these findings, by interrogating RNAseq results from tumor and adjacent normal tissue in clinical specimens of human head and neck squamous carcinoma, we found evidence that TGF-β/Notch crosstalk contributed to progression. In summary, the myeloid cell-carcinoma signaling network we describe uncovers novel mechanistic links between the tumor microenvironment and tumor growth, highlighting new opportunities to target tumors where this network is active.
Framework encapsulations (1998)

Today's complex leading-edge design processes require the use of multiple CAD tools that operate in multiple frameworks making management of the complete design process difficult. This paper introduces the concept of framework encapsulations: software wrappers around complete CAD frameworks that allow the design data and flow management services of a framework to be utilized by a common design process management tool. This concept has been applied to the Minerva II Design Process Manager, enabling Minerva II to manage the design process across multiple CAD frameworks, and potentially multiple design disciplines.
Honey Bee Queen Pheromones and Worker Foraging Behavior1 (1970)

Small colonies of honey bees, Apis mellifera L. (Hymenoptera: Apidae), containing 600 workers were trained to collect syrup from counter-feeders in screened flight cages. Foraging activity was recorded for 2 days while all colonies had caged queens. Some queens were then replaced by porous plastic blocks containing queen extract, synthetic 9-oxodec-trans-2-enoic (9-oxodecenoic) acid, or alcohol. Foraging activity was recorded for 3 more days. Bees from colonies receiving only alcohol flew fewer trips and carried less syrup than those from colonies that received 9-oxodecenoic acid or that retained their queens. Bees receiving extract visited the feeder about as many times as those with alcohol but carried signicantly greater quantities of syrup. Death losses were greatest in colonies that received alcohol and least in those that retained their queen. Field experiments using colonies of about 10,000 workers confirmed the cage results and indicated that pollen foraging is not controlled primarily by queen pheromones as is nectar foraging. In both field and cage experiments, synthetic 9-oxodecenoic acid, at sufficiently high dosage, was an effective substitute for a queen in stimulating nectar foraging.
The refocusing distance of a standard plenoptic photograph (2015)

In the past years, the plenoptic camera aroused an increasing interest in the field of computer vision. Its capability of capturing three-dimensional image data is achieved by an array of micro lenses placed in front of a traditional image sensor. The acquired light field data allows for the reconstruction of photographs focused at different depths. Given the plenoptic camera parameters, the metric distance of refocused objects may be retrieved with the aid of geometric ray tracing. Until now there was a lack of experimental results using real image data to prove this conceptual solution. With this paper, the very first experimental work is presented on the basis of a new ray tracing model approach, which considers more accurate micro image centre positions. To evaluate the developed method, the blur metric of objects in a refocused image stack is measured and compared with proposed predictions. The results suggest quite an accurate approximation for distant objects and deviations for objects closer to the camera device.
N-Heterocyclic Carbene-Catalyzed Generation of Homoenolates:  γ-Butyrolactones by Direct Annulations of Enals and Aldehydes (2004)

N-Heterocyclic carbenes, prepared in situ from diarylimidazolium salts, serve as highly effective catalysts for the generation of reactive homoenolates from alpha,beta-unsaturated aldehydes. The catalyst-bound homoenolate reacts with electrophilic aldehydes leading, via the key intermediacy of an activated carboxylate, to gamma-butyrolactones in good yields and stereoselectivities. Importantly, this process demonstrates an unprecedented reaction mode for the generation of nucleophilic carbanions with a multifunctional organocatalyst under exceptionally mild and convenient reaction conditions.
Achieving optimal attenuation in acoustic waveguides with 3D printed Helmholtz resonators (2021)

A double root, commonly referred to as an exceptional point (EP), for modal frequencies in a 2D or 3D waveguide can exhibit optimal attenuation rates over a relatively broad frequency range. The key to the phenomenon is that the wall impedance is such that modes coalesce at a complex-valued frequency. In this talk we consider a novel approach to feasibly achieve the aforementioned wall impedance with the use of simple resonators, which can be shown to exhibit mode coalescence at distinct frequencies when treated as a unit cell component of a larger metasurface. Numerical results of several unit cell designs are given to test the boundaries on the following constraints: realizable resonator dimensions, scale separation, and target attenuation goals. To validate the analytical work, experimental setups consisting of additively manufactured Helmholtz resonators incorporated onto a custom-made impedance tube are tested. The dependence of printed resonator quality on theoretical inertial, loss, and stiffness values are discussed in tandem with printing repeatability. Simulated finite element model results will be used as comparative backdrops with the numerical and experimental results. Work supported by NSF.
Widespread regulatory activity of vertebrate microRNA* species (2010)

An obligate intermediate during microRNA (miRNA) biogenesis is an ∼22-nucleotide RNA duplex, from which the mature miRNA is preferentially incorporated into a silencing complex. Its partner miRNA* species is generally regarded as a passenger RNA, whose regulatory capacity has not been systematically examined in vertebrates. Our bioinformatic analyses demonstrate that a substantial fraction of miRNA* species are stringently conserved over vertebrate evolution, collectively exhibit greatest conservation in their seed regions, and define complementary motifs whose conservation across vertebrate 3′-UTR evolution is statistically significant. Functional tests of 22 miRNA expression constructs revealed that a majority could repress both miRNA and miRNA* perfect match reporters, and the ratio of miRNA:miRNA* sensor repression was correlated with the endogenous ratio of miRNA:miRNA* reads. Analysis of microarray data provided transcriptome-wide evidence for the regulation of seed-matched targets for both mature and star strand species of several miRNAs relevant to oncogenesis, including mir-17 , mir-34a , and mir-19 . Finally, 3′-UTR sensor assays and mutagenesis tests confirmed direct repression of five miR-19* targets via star seed sites. Overall, our data demonstrate that miRNA* species have demonstrable impact on vertebrate regulatory networks and should be taken into account in studies of miRNA functions and their contribution to disease states.
What Is Concept Drift and How to Measure It (2010)

This paper studies concept drift over time. We first define the meaning of a concept in terms of intension, extension and label. We then introduce concept drift over time and two derived notions: (in)stability over a time period and concept shift between two time points. We apply our framework in three case-studies, one from communication science, on DBPedia, and one in the legal domain. We describe ways of identifying interesting changes in the meaning of concept within given application contexts. These case-studies illustrate the feasibility of our framework in analysing concept drift in knowledge organisation schemas of varying expressiveness.
Exploring how plasma- and muscle-related parameters affect trout hemolysis as a route to prevent hemoglobin-mediated lipid oxidation of fish muscle (2022)

Hemoglobin (Hb) is a powerful promoter of lipid oxidation, particularly in muscle of small pelagic fish species and fish by-products, both having high Hb-levels and highly unsaturated lipids. As Hb is located within the red blood cells (RBCs) it is here hypothesized that the perishable polyunsaturated fatty acids (PUFAs) can be protected from oxidation by limiting hemolysis during early fish processing. Using a model system consisting of washed-resuspended trout (Oncorhynchus mykiss) RBCs (wr-RBCs), the aim of this study was to evaluate how RBC lysis under cold storage was affected by selected parameters linked to blood or muscle: bacterial growth, energy status, pH, RBC membrane lipid oxidation and colloidal osmotic pressure (COP). The results indicated that bacterial growth had a modest effect on hemolysis while pH-values typical for post mortem fish muscle (6.4-6.8), and absence of glucose or albumin stimulated hemolysis. The rapid hemolysis observed at pH 6.4-6.8 correlated with lipid oxidation of the RBC membrane, while the lower hemolysis at pH 7.2-8.0 occurred with low, or without any RBC membrane lipid oxidation. When hemin was added to the RBCs at pH 6.8 hemolysis was induced without parallel RBC membrane oxidation, pointing at Hb-autoxidation and hemin-release per se as important events triggering lysis in fish muscle. Altogether, the study provided valuable findings which ultimately can aid development of new tools to combat lipid oxidation in post mortem fish muscle by limiting hemolysis.
Short Article lin-35 Rb Acts in the Major Hypodermis to Oppose Ras-Mediated Vulval Induction in C. elegans (2005)

Summary Mutations that constitutively activate the inductive or lateral signaling pathways cause ectopic induction of Specification of vulval precursor cell (VPC) fates in P3.p,P4.p,andP8.p.EachoftheseVPCsthengenerates C.elegans hasservedasanimportantsignaltransduc- vulvalcells,whichorganizeintoapseudovulva,thehall- tion paradigm. Genetic studies have indicated that a mark of a multivulva (Muv) phenotype. Mutations in an- large group of synthetic multivulva (SynMuv) genes, other large group of genes, collectively called synthetic includingtheRbortholog lin-35 ,antagonizestheactiv- multivulva (SynMuv) genes, also cause a Muv pheno- ity of the EGF receptor-Ras-MAP kinase pathway dur- type. The SynMuv genes fall into two subgroups, Class ing VPC specification. A prevalent view has been that A and Class B. Single mutants in each class are pheno- Rb-mediatedtranscriptionalregulationandchromatin typicallywild-type,but whenaClassA mutationiscom- remodeling activities act in the VPCs to antagonize
Graphite Microparticles as Coatings for Quartz Crystal Microbalance-Based Gas Sensors (2000)

The use of graphite particles (1-2 microm) as coatings on quartz crystal microbalances (QCMs) for detection and monitoring of toluene and other volatile organic compounds (VOCs) is described. Unlike the more commonly used polymeric coatings with low glass transition temperatures (Tg), particulate graphitic coatings are not as susceptible to loss of acoustic energy when coating thickness or operational temperature increases. This situation enables the use of relatively thick coatings, which increases the absolute amount of vapor sorbed in the coating and, consequently, lowers the level of detection and enhances operation over a wide temperature range. The use of small size particles also results in a coating with a more porous structure, which facilitates uptake and release of VOCs in comparison to coatings made from high Tg polymers, which have a lower porosity. These attributes, coupled with the inherent stability of graphitic materials, make particulate graphite coatings especially suitable for applications at high temperatures. The advantages of using particulate graphite as a coating on QCMs are demonstrated by comparison to the performance of a few low-Tg polymers [i.e., poly(isobutylene) and poly(diphenoxyphosphazene)] and high-Tg polymers (i.e., polystyrene).
A PECULIAR CASE OF MULTIPLE GIGANTIC SEBORRHEIC KERATOSES (1997)

Department of Plastic Surgery; Ancona University School of Medicine; Piazza Cappelli, 1; I-60121 Ancona, Italy
Improvement in Aqueous Solubility of Retinoic Acid Receptor (RAR) Agonists by Bending the Molecular Structure (2016)

Aqueous solubility is a key requirement for many functional molecules, e. g., drug candidates. Decrease of the partition coefficient (log P) by chemical modification, i.e., introduction of hydrophilic group(s) into molecules, is a classical strategy for improving aqueous solubility. We have been investigating alternative strategies for improving the aqueous solubility of pharmaceutical compounds by disrupting intermolecular interactions. Here, we show that introducing a bend into the molecular structure of retinoic acid receptor (RAR) agonists by changing the substitution pattern from para to meta or ortho dramatically enhances aqueous solubility by up to 890-fold. We found that meta analogs exhibit similar hydrophobicity to the parent para compound, and have lower melting points, supporting the idea that the increase of aqueous solubility was due to decreased intermolecular interactions in the solid state as a result of the structural changes.
Preparation and characterization of monoclonal antibodies recognizing three distinct differentiation antigens (BL1, BL2, BL3) on human B lymphocytes. (1984)

We report in this paper the generation and characterization of three monoclonal antibodies, designated alpha BL1, alpha BL2, and alpha BL3, that recognize distinctive antigens unrelated to complement, Fc, and mouse erythrocyte rosette receptors, which are preferentially expressed on B lymphocytes. alpha BL1 recognizes a heat stable nonimmunoprecipitable antigen, possibly glycolipid in nature. Alpha BL2 recognizes a nonreducible single polypeptide with a m.w. of 68,000 that occasionally co-precipitates with a p29,34 complex of HLA-DR antigens. Alpha BL3 recognizes a nonreducible single polypeptide with a m.w. of 105,000 with an acidic pI point. We demonstrated that BL1 is expressed on fetal liver hematopoietic cells, a small subset (5 to 15%) of Ficoll-Hypaque-separated normal bone marrow cells, and on a subpopulation of nonadherent, non-E rosette-forming cells and granulocytes. BL2 is expressed on fetal liver hematopoietic cells, on 3 to 7% of normal bone marrow cells, and on a majority (40 to 70%) of nonadherent, non-E rosette-forming cells with a distinctive pattern similar to that of HLA-DR. BL3 is expressed on a subpopulation of nonadherent, non-E rosette-forming cells, and on occasional cells in the monocyte-enriched adherent cell population. The peak fluorescence for BL2 is substantially higher than that of BL1 and BL3, indicating higher BL2 antigen density. All three antigens are absent from thymocytes and E rosette-positive T cell fractions obtained from various lymphoid tissues. Cellular distribution of the BL antigens on various well-characterized established hematopoietic cell lines, leukemias, and malignant lymphomas, in conjunction with the results of the in vitro activation and TPA-induction experiments, suggest that BL1 is expressed during early developmental stages of B cell differentiation, whereas BL3 is expressed at the later stages. BL2 expression spans immature and mature stages of B cell differentiation, with the exception of mature plasma cells. The alpha BL antibodies described here should prove to be useful in the investigation of B cell differentiation and in the clinical diagnosis of lymphoid neoplasms.
Inflammation and risk of recurrent vascular events after TIA and minor stroke: the NORTHSTAR study (2009)

The liver-related mortality rate increased significantly, even in CHB patients with relatively low serum ALT levels. Careful monitoring or earlier antiviral therapy should be considered for patients aged >40 years with serum ALT levels above the upper limit of normal.
Consistency for web services applications (2005)

A key challenge facing the designers of service-oriented applications is ensuring that the autonomous services that make up these distributed applications always finish in consistent states despite application-level failures and other exceptional events. This paper addresses this problem by first describing the relationship between internal service states, messages and application protocols and then shows how this relationship transforms the problem of ensuring consistent outcomes into a correctness problem that can be addressed with established protocol verification tools.
Persistent array access using server-directed I/O (2002)

Large multidimensional arrays are a common data type in high-performance scientific applications. Without special techniques for handling access to these arrays, I/O can easily become a large fraction of execution time for applications using these arrays, especially on parallel platforms. We show how to reduce the parallel I/O bottleneck for array data in closely-synchronized SPMD applications on distributed-memory platforms, through the use of server-directed I/O. This method allows array data requests on parallel platforms to be translated into long sequential disk reads and writes, while also minimizing the cost of rearranging data as they move between on-disk and in-memory schemas. We present experimental results from the implementation of server-directed I/O in Panda, showing that for I/O of large arrays, Panda utilizes nearly the maximum throughput of the underlying AIX file system on an IBM SP2. We also discuss Panda's user interface, an essential factor in Panda's high performance.
Photocatalytic and bactericidal properties and molecular docking analysis of TiO2nanoparticles conjugated with Zr for environmental remediation (2020)

Despite implementing several methodologies including a combination of physical, chemical and biological techniques, aquatic and microbial pollution remains a challenge to this day. Recently, nanomaterials have attracted considerable attention due to their extraordinary prospective for utilization toward environmental remediation. Among several probable candidates, TiO<sub>2</sub> stands out due to its potential for use in multifaceted applications. One way to improve the catalytic and antimicrobial potential of TiO<sub>2</sub> is to dope it with certain elements. In this study, Zr-doped TiO<sub>2</sub> was synthesized through a sol-gel chemical method using various dopant concentrations (2, 4, 6, and 8 wt%). Surface morphological, microstructural and elemental analysis was carried out using FESEM and HR-TEM along with EDS to confirm the formation of Zr-TiO<sub>2</sub>. XRD spectra showed a linear shift of the (101) anatase peak to lower diffraction angles (from 25.4° to 25.08°) with increasing Zr<sup>4+</sup> concentration. Functional groups were examined <i>via</i> FTIR, an ample absorption band appearing between 400 and 700 cm<sup>-1</sup> in the acquired spectrum was attributed to the vibration modes of the Ti-O-Ti linkage present within TiO<sub>2</sub> nanoparticles, which denotes the formation of TiO<sub>2</sub>. Experimental results indicated that with increasing dopant concentrations, photocatalytic potential was enhanced significantly. In this respect, TiO<sub>2</sub> doped with 8 wt% Zr (sample 0.08 : 1) exhibited outstanding performance by realizing 98% elimination of synthetic MB in 100 minutes. This is thought to be due to a decreased rate of electron-hole pair recombination that transpires upon doping. Therefore, it is proposed that Zr-doped TiO<sub>2</sub> can be used as an effective photocatalyst material for various environmental and wastewater treatment applications. The good docking scores and binding confirmation of Zr-doped TiO<sub>2</sub> suggested doped nanoparticles as a potential inhibitor against selected targets of both <i>E. coli</i> and <i>S. aureus</i>. Hence, enzyme inhibition studies of Zr-doped TiO<sub>2</sub> NPs are suggested for further confirmation of these <i>in silico</i> predictions.
Data on the anti-tumor effects of Selaginella tamariscina extract and amentoflavone combined with doxorubicin in mice (2017)

Here, we report animal experimental data associated with the article entitled "AKR1B10-inhibitory <i>Selaginella tamariscina</i> extract and amentoflavone decrease the growth of A549 human lung cancer cells in vitro and in vivo" (Jung et al., 2017) [1]. We tested the synergistic anti-tumor effects of <i>Selaginella tamariscina</i> extract and amentoflavone combined with doxorubicin hydrochloride in a nude mouse xenograft model of A549 human lung cancer cells. In our experiment, <i>Selaginella tamariscina</i> extract and amentoflavone were administered orally; and doxorubicin hydrochloride was injected intraperitoneally. We expect our preliminary data will be helpful to the development of the anticancer agent using <i>Selaginella tamariscina</i> extract or amentoflavone.