gebhart/patrepeval huggingface dataset:
Polycystins and mechanosensation in renal and nodal cilia (2004)

The external surfaces of the human body, as well as its internal organs, constantly experience different kinds of mechanical stimulations. For example, tubular epithelial cells of the kidney are continuously exposed to a variety of mechanical forces, such as fluid flow shear stress within the lumen of th nephron. The majority of epithelial cells along the nephron, except intercalated cells, possess a primary cilium, an organelle projecting from the cell's apical surface into the luminal space. Despite its discovery over 100 years ago, the primary cilium's function continued to elude researchers for many decades. However, recent studies indicate that renal cilia have a sensory function. Studies on polycystic kidney disease (PKD) have identified many of the molecular players, which should help solve the mystery of how the renal cilium senses fluid flow. In this review, we will summarize the recent breakthroughs in PKD research and discuss the role(s) of the polycystin signaling complex in mediating mechanosensory function by the primary cilium of renal epithelium as well as of the embryonic node.
Long-chain Omega-3 Polyunsaturated Fatty Acids: Prospects for Introduction into Horticultural Food Plants (1990)

Recent data indicate that significant health benefits may be attributable to the dietary uptake of long-chain omega-3 polyunsaturated fatty acids, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). In this paper we describe current data relating lo the nutritional significance of these compounds, their oc currence in nature and in the human food chain, data related to their biosynthesis, and the prospects for their introduction into horticultural food plants. EPA and DHA are members of a family of fatty acids, designat ed collectively as “omega-3” (also notated as n-3) fatty acids, sodesignated because the first of the recurrent double bonds is three carbons from the methyl terminal. This general class of compounds is often referred to as PUFAs (“polyunsaturated fatty acids”), while the 20 and 22 carbon members of this group are sometimes referred to as HUFAs (“highly unsaturated fatty acids”).
Electronic properties of straight, kinked, and branchedCu∕Cu(111)quantum wires: A low-temperature scanning tunneling microscopy and spectroscopy study (2006)

Low-temperature scanning tunneling microscopy at $7\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ is used to assemble monatomic native adatom chains on a Cu(111) surface and to study their $sp$-derived quantum states. The adatoms within the structure reside on equivalent nearest-neighbor lattice sites of the substrate surface (intrinsic Cu-Cu spacing $2.55\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$). Starting from linear chain segments, kinked chains and triple-terminal junctions are created, and the impact of the different structural details of the junction on the electronic properties is investigated by spectroscopic measurements. A simple tight-binding (TB) parametrization scheme is applied to discuss the experimentally observed energies and densities of the quantum states inherent to these chain structures of advanced complexity. The TB model also reveals potential overlaps of resonance-broadened states, which are not resolved in the experiment.
Air Foam Improves Efficiency of Completion and Workover Operations in Low-Pressure Gas Wells (1995)

Summary Air foam has developed into a cost-effective alternative to nitrogen foam for completion and workover operations in low-pressure gas wells. In most cases, air foam represents less than one-third the cost of nitrogen and is being used with increasing frequency in the Texas/ Oklahoma Panhandle region of the U.S. This paper addresses the three traditional concerns associated with the use of air foam: (1) lower available pressures and rates, (2) flammability, and (3) corrosion. The paper also details the use of these portable air-foam units in circulating operations, including coiled tubing. Newer applications are discussed where air foam can reduce costs compared with swabbing. Experimental results demonstrate that air foam can be used at circulating temperatures up to 120°F with commercially available corrosion inhibitors. We show that extension of air foam to deep wells with temperatures up to 350°F is possible with a newly developed inhibitor.
BlueTable (2007)

Associating and connecting mobile devices for the wireless transfer of data is often a cumbersome process. We present a technique of associating a mobile device to an interactive surface using a combination of computer vision and Bluetooth technologies. Users establish the connection of a mobile device to the system by simply placing the device on a table surface. When the computer vision process detects a phone-like object on the surface, the system follows a handshaking procedure using Bluetooth and vision techniques to establish that the phone on the surface and the wirelessly connected phone are the same device. The connection is broken simply by removing the device. Furthermore, the vision-based handshaking procedure determines the precise position of the device on the interactive surface, thus permitting a variety of interactive scenarios which rely on the presentation of graphics co-located with the device. As an example, we present a prototype interactive system which allows the exchange of automatically downloaded photos by selecting and dragging photos from one cameraphone device to another.
N7: A novel multi-modality therapy of high risk neuroblastoma (NB) in children diagnosed over 1 year of age (2001)

Major toxicities were grade 4 myelosuppression and mucositis during chemotherapy, and self-limited pain and urticaria during antibody treatment. Late effects include hearing deficits and hypothyroidism.
Inducers of erythroleukemic differentiation. Relationship of structure to activity among planar-polar compounds. (1978)

Hexamethylenebisacetamide is a potent inducer of erythroid differentiation in murine erythroleukemia cells. A series of chemical compounds structurally related to hexamethylenebisacetamide were tested for inducing activity including polymethylene chains terminally substituted with various combinations of carboxylate, amino, amide, or sulfoxide groups. Effective "dimerization" of dimethyl sulfoxide through a linear polymethylene chain increases its inducing activity by a magnitude similar to that observed when N-methylacetamide is effectively dimerized in such a manner. It was found that all potent inducing agents possess both a hydrophilic and hydrophobic portion of the molecule, as well as a planar portion. All are Lewis bases, possessing a free electron pair available for hydrogen bonding. The polymethylene chain joining functional groups must be flexible and must be 5 to 6 carbon atoms in length to achieve maximal activity. Introduction of triple or double (cis or trans) bonds into the polymethylene chain does not alter activity.
Expanding the CRISPR imaging toolset withStaphylococcus aureusCas9 for simultaneous imaging of multiple genomic loci (2016)

In order to elucidate the functional organization of the genome, it is vital to directly visualize the interactions between genomic elements in living cells. For this purpose, we engineered the Cas9 protein from Staphylococcus aureus (SaCas9) for the imaging of endogenous genomic loci, which showed a similar robustness and efficiency as previously reported for Streptococcus pyogenes Cas9 (SpCas9). Imaging readouts allowed us to characterize the DNA-binding activity of SaCas9 and to optimize its sgRNA scaffold. Combining SaCas9 and SpCas9, we demonstrated two-color CRISPR imaging with the capability to resolve genomic loci spaced by <300 kb. Combinatorial color-mixing further enabled us to code multiple genomic elements in the same cell. Our results highlight the potential of combining SpCas9 and SaCas9 for multiplexed CRISPR-Cas9 applications, such as imaging and genome engineering.
The Evolving Biomarker Landscape for Treatment Selection in Metastatic Colorectal Cancer (2019)

The approval of targeted therapies for metastatic colorectal cancer (mCRC) has led to important improvements in patient outcomes. However, it is still necessary to increase individualisation of treatments based on tumour genetic profiles to optimise efficacy, while minimising toxicity. As such, there is currently great focus on the discovery and validation of further biomarkers in mCRC, with many new potential prognostic and predictive markers being identified alongside developments in patient molecular profiling technologies. Here, we review data for validated and emerging biomarkers impacting treatment strategies in mCRC. We completed a structured literature search of the PubMed database to identify relevant publications, limiting for English-language publications published between 1 January 2014 and 11 July 2018. In addition, we performed a manual search of the key general oncology and CRC-focused congresses to identify abstracts reporting emerging mCRC biomarker data, and of ClinicalTrials.gov to identify ongoing clinical trials investigating emerging biomarkers in mCRC and/or molecular-guided clinical trials. There is solid evidence supporting the use of BRAF status as a prognostic biomarker and DYPD, UGT1A1, RAS, and microsatellite instability as predictive biomarkers in mCRC. There are a number of emerging biomarkers that may prove to be clinically relevant in the future to have prognostic (HPP1 methylation), predictive (HER3, microRNAs, anti-angiogenic markers, and CRC intrinsic subtypes), or both prognostic and predictive values (HER2, CpG island methylator phenotype, tumour mutational load, gene fusions, and consensus molecular subtypes). As such, new biomarker-led treatment strategies in addition to anti-epidermal growth factor receptor and anti-angiogenetic treatments are being explored. Biomarkers that are not recommended to be tested in clinical practice or are unlikely to be imminently clinically relevant for mCRC include thymidylate transferase, ERCC1, PIK3CA, and PTEN. We highlight the clinical utility of existing and emerging biomarkers in mCRC and provide recommended treatment strategies according to the biomarker status. An update on ongoing molecular-guided clinical trials is also provided.
Marine debris observed in the North Pacific during Oshoro-maru cruise in 2012 (2014)

The distribution and abundance of marine debris were investigated by visual survey and a neuston net in the North Pacific and Bering Sea during the T/S Oshoro Maru cruise from June to August 2012. The observed debris included pieces of plastic, plastic and glass bottles, metallic objects, glass, and fishing gear. The concentrations of plastic sampled by a neuston net were higher in the Transition Zone than those in the Subarctic North Pacific and Bering Sea. The abundance and weight of these small plastic pieces collected by a neuston net did not significantly increase from 1980s. Long-term monitoring and information sharing are important in concert with related countries and organizations.
BER-H2: a new anti-Ki-1 (CD30) monoclonal antibody directed at a formol- resistant epitope (1989)

The production and characterization of a monoclonal antibody (MoAb) designated Ber-H2, directed against a new epitope of the Ki-1 (CD30) antigen, are described. In comparison with the formerly reported Ki-1 MoAb whose reactivity with Hodgkin and Reed-Sternberg (H-RS) cells in frozen tissue sections is well-documented, the Ber-H2 MoAb showed new, important features: the labeling intensity of the Ber-H2 MoAb was much stronger, and the number of positively labeled cells was higher. Most important, however, was that the Ber-H2 MoAb could be applied in routinely processed, formaldehyde-fixed, paraffin-embedded tissue sections. Therefore, it was possible to investigate an unprecedented number of tumors received as frozen or formaldehyde-fixed material for expression of the CD30 antigen. Beside Hodgkin's disease, the Ber-H2 MoAb labeled a variable number of cells in lymphomatoid papulosis, peripheral T-cell lymphomas, and angoimmunoblastic lymphadenopathy. Among B-cell non-Hodgkin's lymphomas (NHLs), some cases containing large centroblast-like or immunoblast-like cells or displaying plasma-cellular differentiation were positive. This finding was in keeping with the reactivity of the Ber-H2 MoAb with activated B-cell blasts and a subpopulation of plasma cells in paraffin sections of normal lymphoid tissue. The diagnostic value of the Ber-H2 MoAb was most significant for a group of anaplastic large-cell (ALC) lymphomas (formerly frequently referred to as malignant histiocytosis or regressive atypical histiocytosis), of which more than 50 cases could be investigated, owing to applicability in paraffin sections. Although about one third of these ALC lymphomas did not express the leukocyte common (CD45) antigen, they were consistently reactive with the Ber-H2 MoAb in both frozen and paraffin-embedded tissue sections. Using the Ber-H2 MoAb, these Ki-1 lymphomas could be easily distinguished from other nonlymphoid anaplastic large-cell tumors.
Mouse lymphoma cell lines resistant to pea lectin are defective in fucose metabolism. (1980)

Two mutants of the BW5147 mouse lymphoma cell line have been selected for their resistance to the toxic effects of pea lectin. These cell lines, termed PLR1.3 and PHAR1.8 PLR7.2, have a decreased number of high affinity pea lectin-binding sites (Trowbridge, I.S., Hyman, R., Ferson, T., and Mazauskas, C. (1978) Eur. J. Immunol. 8, 716-723). Intact cell labeling experiments using [2-3H]mannose indicated that PLR1.3 cells have a block in the conversion of GDP-[3H]mannose to GDP-[3H]fucose whereas PHAR1.8 PLR7.2 cells appear to be blocked in the transfer of fucose from GDP-[3H]fucose to glycoprotein acceptors. In vitro experiments with extracts of PLR1.3 cells confirmed the failure to convert GDP-mannose to GDP-fucose and indicated that the defect is in GDP-mannose 4,6-dehydratase (EC 4.2.1.47), the first enzyme in the conversion of GDP-mannose to GDP-fucose. The block in the PLR1.3 cells could be bypassed by growing the cells in the presence of fucose, demonstrating that an alternate pathway for the production of GDP-fucose presumably via fucose 1-phosphate is functional in this line. PLR1.3 cells grown in 10 mM fucose showed normal high affinity pea lectin binding. PHRA1.8 PLR7.2 cells synthesize GDP-fucose and have normal or increased levels of GDP-fucose:glycoprotein fucosyltransferase when assayed in vitro. The fucosyltransferases of this clone can utilize its own glycoproteins as fucose acceptors in in vitro assays. These findings indicate that this cell line fails to carry out the fucosyltransferase reaction in vivo despite the fact that it possesses the appropriate nucleotide sugar, glycoprotein acceptors, and fucosyltransferase. The finding of decreased glycoprotein fucose in two independent isolates of pea lectin-resistant cell lines and the restoration of high affinity pea lectin binding to PLR1.3 cells following fucose feeding strongly implicates fucose as a major determinant of pea lectin binding.
Polymer Refilling of Presbyopic Human Lenses In Vitro Restores the Ability to Undergo Accommodative Changes (2003)

Refilling presbyopic lenses with a soft polymer enabled restoration of lens power changes with mechanical stretching. Because sclerosis of the lens is an important factor in human presbyopia, refilling the lens during lens surgery for cataract could enable restoration of clear vision and accommodation in human presbyopia.
An fMRI-Based Neurologic Signature of Physical Pain (2013)

It is possible to use fMRI to assess pain elicited by noxious heat in healthy persons. Future studies are needed to assess whether the signature predicts clinical pain. (Funded by the National Institute on Drug Abuse and others.).
Decoherence and the Transition from Quantum to Classical (1991)

Quantum mechanics works exceedingly well in all practical applications. No example of conflict between its predictions and experiment is known. Without quantum physics we could not explain the behavior of solids, the structure and function of DNA, the color of the stars, the action of lasers or the properties of superfluids. Yet well over half a century after its inception, the debate about the relation of quantum mechanics to the familiar physical world continues. How can a theory that can account ith precision for everything we can measure still be deemed lacking?
Phellodendron amurenseand Its Major Alkaloid Compound, Berberine Ameliorates Scopolamine-Induced Neuronal Impairment and Memory Dysfunction in Rats (2012)

We examine whether Phellodendron amurense (PA) and its major alkaloid compound, berberine (BER), improved memory defects caused by administering scopolamine in rats. Effects of PA and BER on the acetylcholinergic system and pro-inflammatory cytokines in the hippocampus were also investigated. Male rats were administered daily doses for 14 days of PA (100 and 200 mg/kg, i.p.) and BER (20 mg/kg, i.p.) 30 min before scopolamine injection (2 mg/kg, i.p.). Daily administration of PA and BER improved memory impairment as measured by the passive avoidance test and reduced the escape latency for finding the platform in the Morris water maze test. Administration of PA and BER significantly alleviated memory-associated decreases in cholinergic immunoreactivity and restored brain-derived neurotrophic factor and cAMP-response element-binding protein mRNA expression in the hippocampus. PA and BER also decreased significantly the expression of proinflammatory cytokines such as interleukin-1β, tumor necrosis factor-α and cyclooxygenase-2 mRNA in the hippocampus. These results demonstrated that PA and BER had significant neuroprotective effects against neuronal impairment and memory dysfunction caused by scopolamine in rats. These results suggest that PA and BER may be useful as therapeutic agents for improving cognitive functioning by stimulating cholinergic enzyme activity and alleviating inflammatory responses.
Design and characterization of an air-coupled capacitive ultrasonic sensor fabricated in a CMOS process (2007)

This work presents a CMOS micromachined capacitive sensor for the detection of acoustic pressure transmitted through the air. The microstructure has a suspended plate of 65 µm in diameter that produces a sensing capacitance of 35 fF and a resonant frequency of 1.2 MHz. The post-CMOS fabrication can effectively reduce the parasitic capacitance to enhance the signal-to-noise ratio. The measured input-referred circuit noise is 0.35 µV Hz1/2 at 40 kHz. The measured sensor output is 3.5 µV under a dc bias of 10 V, equivalent to a capacitance change of 1.7 × 10−2 aF. The corresponding electrode displacement and acoustic pressure are 4.1 × 10−2 Å and 1.3 Pa, respectively.
Left Vagus Nerve Stimulation with the Neurocybernetic Prosthesis Has Complex Effects on Heart Rate and on Its Variability in Humans (2001)

LVNS at high intensities has complex effects on IHR and HRV, which show large interindividual variability. These spectra of cardiac responses reflect the interplay of autonomic, visceral, and somatic sensory afferences and the role of central structures in their integration. These findings also point to the need for more comprehensive studies of cardiac function in humans implanted with the NCP, using sensitive methods for data processing and analysis such as those developed for this study.
Vascularization of normal and neoplastic tissues grafted to the chick chorioallantois. Role of host and preexisting graft blood vessels. (1975)

Adult, embryonic, and tumor tissues were grafted to the chorioallantoic membrane of the chick embryo to determine whether blood vessels originally within implants were reused in the establishment of a new blood supply. Grafts were examined daily by in vivo stereomicroscopy and in histologic sections. Colloidal carbon injections into the host vasculature served to confirm the precise onset of graft circulation; Preexisting tumor blood vessels disintegrated by 24 hours after implantation and revascularization occurred at 3 days by penetration of proliferating host vessels into the tumor tissue. Adult tissues did not revascularize, and the original graft vasculature progressively disintegrated during the 9 days of observation, Most embryonic tissues revascularized in 1 or 2 days by reperfusion of the existing graft vasculature. Anastomosis of host and graft blood vessels seemed to result from connections between newly formed vascular sprouts arising from both vasculatures. This study indicates that only tumor grafts acquire their blood supply solely by formation of new blood vessels from the host microvasculature. By contrast revascularization of normal tissues, when it does occur, is predominately the result of perfusion of the preexisting graft blood vessels.
Version Control with Git (2009)

Get up to speed on Git for tracking, branching, merging, and managing code revisions. Through a series of step-by-step tutorials, this practical guide takes you quickly from Git fundamentals to advanced techniques, and provides friendly yet rigorous advice for navigating the many functions of this open source version control system. This thoroughly revised edition also includes tips for manipulating trees, extended coverage of the reflog and stash, and a complete introduction to the GitHub repository. Git lets you manage code development in a virtually endless variety of ways, once you understand how to harness the system's flexibility. This book shows you how. Learn how to use Git for several real-world development scenarios ; Gain insight into Git's common-use cases, initial tasks, and basic functions ; Use the system for both centralized and distributed version control ; Learn how to manage merges, conflicts, patches, and diffs ; Apply advanced techniques such as rebasing, hooks, and ways to handle submodules ; Interact with Subversion (SVN) repositories-including SVN to Git conversions ; Navigate, use, and contribute to open source projects though GitHub.
Topical Bevacizumab in the Treatment of Corneal Neovascularization (2009)

clinicaltrials.gov Identifier: NCT00559936.
Synergistic antitumor responses by combined GITR activation and sunitinib in metastatic renal cell carcinoma (2015)

Sunitinib, a multitargeted tyrosine kinase inhibitor, is the frontline therapy for renal and gastrointestinal cancers. In view of its well-documented proapoptotic and immunoadjuvant properties, we speculate that combination of Sunitinib and immunotherapy would provide a synergistic antitumor effect. Here, we report that a remarkably synergistic antitumor responses elicited by the combined treatment of Sunitinib and an agonistic antibody against glucocorticoid-induced TNFR related protein (GITR) in a model of metastatic renal cell carcinoma. Sunitinib significantly increased the infiltration, activation, and proliferation and/or cytotoxicity of CD8(+) T cells and NK cells in liver metastatic foci when combined with the anti (α)-GITR agonist, which was associated with treatment-induced prominent upregulation of Th1-biased immune genes in the livers from mice receiving combined therapy versus single treatment. Sunitinib/α-GITR treatment also markedly promoted the maturation, activation and cytokine production of liver-resident macrophages and DCs compared with that achieved by α-GITR or Sunitinib treatment alone in mice. Cell depletion experiments demonstrated that CD8(+) T cells, NK cells and macrophage infiltrating liver metastatic foci all contribute to the antitumor effect induced by combined treatment. Furthermore, mechanistic investigation revealed that Sunitinib treatment reprograms tumor-associated macrophages toward classically activated or "M1" polarization upon GITR stimulation and consequently mounts an antitumor CD8(+) T and NK cell response via inhibiting STAT3 activity. Thus, our findings provide a proof of concept that Sunitinib can synergize with α-GITR treatment to remodel the tumor immune microenvironment to trigger regressions of an established metastatic cancer.