gebhart/patrepeval huggingface dataset:
Whole-Mount MeFISH: A Novel Technique for Simultaneous Visualization of Specific DNA Methylation and Protein/RNA Expression (2014)

To understand the spatiotemporal changes in cellular status that occur during embryonic development, it is desirable to detect simultaneously the expression of genes, proteins, and epigenetic modifications in individual embryonic cells. A technique termed methylation-specific fluorescence in situ hybridization (MeFISH) was developed recently that can visualize the methylation status of specific DNA sequences in cells fixed on a glass slide. Here, we adapted this glass slide-based MeFISH to the study of intact embryos, and established a method called whole-mount MeFISH. This method can be applied to any DNA sequences in theory and, as a proof-of-concept experiment, we examined the DNA methylation status of satellite repeats in developing mouse primordial germ cells, in which global DNA demethylation is known to take place, and obtained a result that was consistent with previous findings, thus validating the MeFISH method. We also succeeded in combining whole-mount MeFISH with immunostaining or RNA fluorescence in situ hybridization (RNA-FISH) techniques by adopting steps to retain signals of RNA-FISH or immunostaining after harsh denaturation step of MeFISH. The combined methods enabled the simultaneous visualization of DNA methylation and protein or RNA expression at single-cell resolution without destroying embryonic and nuclear structures. This whole-mount MeFISH technique should facilitate the study of the dynamics of DNA methylation status during embryonic development with unprecedented resolution.
<title>Feasibility studies of electrical impedance spectroscopy for monitoring tissue response to photodynamic therapy</title> (1998)

Electrical impedance spectroscopy (EIS) has been evaluated as a non- or minimally-invasive technique to monitor the acute tissue response to photodynamic therapy (PDT). In this study the EIS spectra of normal muscle tissue in the rat hind leg were monitored immediately before and at time intervals up to 96 hours post-PDT treatment with different photosensitizers (Photofrin, ALA-induced PpIX, BenzoPorphyrin Derivative), at varying photosensitizer and light doses. EIS measurements were made using a pair of solid matrix Ag-AgCl electrodes placed parallel to one another on either side of the muscle mass and interfaced to a precision LCR impedance meter scanning the frequency range 1 - 1000 KHz. Independent histological grading of tissue injury was performed on tissue sections from treated and untreated legs at the 96 hour end point. Significant and PDT dose-dependent changes in the EIS spectra following treatment were observed, including increases in conductivity which correlated with the immediate post-PDT edematous response with Photofrin and ALA and which resolved or partially-resolved over the measurement time course. Photofrin treatments exhibited a clear drug dose response at 96 hours that was evident in both the EIS spectra and the histological sections. These changes included significant tissue necrosis as well as edema, inflammation and early fibroplasia. The BPD data were less clear, but potentially quite interesting. Most striking were below unity ratios of treated-to-untreated muscle spectra components at 24 hours which reversed to above unity by 96 hours in the through skin measurements. This phenomenon is indicative of a tissue response distinctly different than that observed with Photofrin or ALA. These data also suggest that EIS measured changes are sensitive enough to detect differences in PDT-initiated tissue damage that may be photosensitize-specific. While the data are derived from a small number of animals, the findings are quite encouraging in terms of the potential for EIS to track PDT-induced changes in tissue.
Pressure Injection on a Valved Microdevice for Electrophoretic Analysis of Submicroliter Samples (2005)

A recent report describes a reversible valve that can be used in series to achieve diaphragm pumping on chip (Grover, W. H.; Skelley, A. M.; Liu, C. N.; Lagally, E. T.; and Mathies, R. A. Sens. Actuators, B 2003, 89, 315-323). Here, the functionality of an integrated diaphragm pump on a hybrid PDMS-glass microchip to perform pressure injections for electrophoretic separations is demonstrated. A chip design that can perform both pressure and electrokinetic (EK) injection is described, and a mixture of fluorescein and ROX dyes in borate buffer is utilized as a model sample system. Multiple electrophoretic separations of sample injected with pressure and voltage are compared. Over multiple EK injections, an electrophoretic bias is observed and the injected analytes are not representative of the sample, with the peak area ratio changing 20% after 20 runs. Over multiple pressure injections, however, the sample composition is maintained, with a 3.6% CV over 20 runs. The data presented show the ability to alternate between injection types and pressure-inject a representative sample volume after a bias has already been observed with multiple EK injections. Multiple pressure injections have been performed on sample volumes as low as 500 nL while maintaining sample composition, supporting its use in integrated systems for small-volume sampling.
Multiwavelength ring networks for switch consolidation and interconnection (2003)

The authors investigate self-healing ring networks that utilize wavelength-division multiplexing (WDM) to provide survivable transport without the need for high-speed electronic add-drop multiplexers. They propose three specific multiwavelength ring networks, two designed for consolidation of switching resources at a single node on the ring, and one that supports symmetrical interconnection between all pairs of nodes. The maximum number of nodes and the maximum total capacity for the three networks are compared, as governed by the characteristics of the optical amplifiers and WDM techniques employed. It is found that all three networks are capable of supporting on the order of ten or more nodes with throughputs of 2.5 Gb/s to 10 Gb/s per node. The descriptions of the proposed networks assume an interoffice-network application, in which the nodes on the ring are central offices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Skp2 inhibits FOXO1 in tumor suppression through ubiquitin-mediated degradation (2005)

Forkhead transcription factors FOXO1 (FKHR), FOXO3a (FKHRL1), and FOXO4 (AFX) play a pivotal role in tumor suppression by inducing growth arrest and apoptosis. Loss of function of these factors due to phosphorylation and proteasomal degradation has been implicated in cell transformation and malignancy. However, the ubiquitin ligase necessary for the ubiquitination of the FOXO factors and the relevance of this regulation to tumorigenesis have not been characterized. Here we demonstrate that Skp2, an oncogenic subunit of the Skp1/Cul1/F-box protein ubiquitin complex, interacts with, ubiquitinates, and promotes the degradation of FOXO1. This effect of Skp2 requires Akt-specific phosphorylation of FOXO1 at Ser-256. Moreover, expression of Skp2 inhibits transactivation of FOXO1 and abolishes the inhibitory effect of FOXO1 on cell proliferation and survival. Furthermore, expression of the FOXO1 protein is lost in a mouse lymphoma model, where Skp2 is overexpressed. These data suggest that the Skp2-promoted proteolysis of FOXO1 plays a key role in tumorigenesis.
The actuated Workbench : 2D actuation in tabletop tangible interfaces (2003)

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2003.
An Overview: Peak-to-Average Power Ratio Reduction Techniques for OFDM Signals (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> One of the challenging issues for Orthogonal Frequency Division Multiplexing (OFDM) system is its high Peak-to-Average Power Ratio (PAPR). In this paper, we review and analysis different OFDM PAPR reduction techniques, based on computational complexity, bandwidth expansion, spectral spillage and performance. We also discuss some methods of PAPR reduction for multiuser OFDM broadband communication systems. </para>
Standardizing Clinically Meaningful Outcome Measures Beyond HbA1c for Type 1 Diabetes: A Consensus Report of the American Association of Clinical Endocrinologists, the American Association of Diabetes Educators, the American Diabetes Association, the Endocrine Society, JDRF International, The Leona M. and Harry B. Helmsley Charitable Trust, the Pediatric Endocrine Society, and the T1D Exchange (2017)

The Steering Committee recommends use of the defined clinically meaningful outcomes beyond HbA<sub>1c</sub> in the research, development, and evaluation of type 1 diabetes therapies.
Cloning and characterization of the cDNA encoding the PH20 protein in the European red fox Vulpes vulpes (1998)

The PH20 protein is thought to play a crucial role in mammalian fertilization. The fox PH20 homologue has been cloned from a testis cDNA library and the deduced protein sequence shows high levels of homology to PH20 proteins isolated from other species. Unlike other PH20 proteins the fox protein does not appear to be membrane associated through a GPI-linkage nor does it show the presence of a transmembrane domain at the C-terminus of the protein. It is in this region that the proteins appear to be least conserved. Immunolocalization studies on fox sperm show that the PH20 protein is located on the inner acrosomal membrane. Transcription of PH20 in the fox is seasonally regulated, with the mRNA expressed during those months when spermatogenesis is at its peak. The PH20 sequence described in this paper has been submitted to the Genbank database and has the accession number U41412.
Growth of Syntrophic Propionate-Oxidizing Bacteria with Fumarate in the Absence of Methanogenic Bacteria (1993)

Oxidation of succinate to fumarate is an energetically difficult step in the biochemical pathway of propionate oxidation by syntrophic methanogenic cultures. Therefore, the effect of fumarate on propionate oxidation by two different propionate-oxidizing cultures was investigated. When the methanogens in a newly enriched propionate-oxidizing methanogenic culture were inhibited by bromoethanesulfonate, fumarate could act as an apparent terminal electron acceptor in propionate oxidation. C-nuclear magnetic resonance experiments showed that propionate was carboxylated to succinate while fumarate was partly oxidized to acetate and partly reduced to succinate. Fumarate alone was fermented to succinate and CO(2). Bacteria growing on fumarate were enriched and obtained free of methanogens. Propionate was metabolized by these bacteria when either fumarate or Methanospirillum hungatii was added. In cocultures with Syntrophobacter wolinii, such effects were not observed upon addition of fumarate. Possible slow growth of S. wolinii on fumarate could not be demonstrated because of the presence of a Desulfovibrio strain which grew rapidly on fumarate in both the absence and presence of sulfate.
Do the Genes That Cause Otosclerosis Reduce Susceptibility to Otitis Media? (2003)

The incidence of chronic otitis media in subjects with a surgically confirmed diagnosis of otosclerosis is significantly lower than expected. The genes that cause otosclerosis may confer resistance to the pathogens that cause chronic otitis media and/or acute otitis media. The mechanism of resistance is unknown.
Promises kept, promises broken: an axiomatic and quantitative treatment of fulfillment (2008)

In this paper, we propose a theoretical framework within which to evaluate the reliability of promises that an agent makes, based on past performance of the agent. Our framework does not just propose one such measure, but defines axioms that govern the choice of measure. The framework is able to account for partial fulfillment of promises, late fulfillment of promises, fulfillment of variants of promises, and the like. Within this framework, we propose some specific measures to evaluate promises made by agents and develop algorithms to compute these efficiently. We tested our methods on a real world data set of airline flight information and show that our methods are both accurate and quickly computable, even on large data sets.
Complement Activation Triggered by Biomaterial Surfaces : Mechanisms and Regulation (2003)

Today there are a vast number of medical devices in temporary or permanent contact with human tissues. Blood-biomaterial contact is known to trigger the complement system and results in generation of fluid phase anaphylatoxins C3a and C5a, and surface-bound C3b and iC3b. All these products together are able to attract and activate leukocytes and trigger release of inflammatory mediators leading to a systemic inflammation indirectly causing hemostatic problems and even organ failure. The aim of this study was to identify how complement is triggered on a biomaterial surface and to find ways to regulate this activation. The finding that complement activation on biomaterials can be divided into initiation and amplification will facilitate regulation of complement activation biomaterial surfaces. This concept is also compatible with the two techniques to regulate complement activation on a surface.
Correlation of cholinergic abnormalities with senile plaques and mental test scores in senile dementia. (1978)

Necropsy brain tissue from normal (control) patients and patients with depression and dementia was examined for activities of various cholinergic components, and these related to the degree of senile plaque formation and extent of intellectual impairment. Choline acetyltransferase and acetylcholinesterase activities decreased significantly as the mean plaque count rose, and in depressed and demented subjects the reduction in choline acetyltransferase activity correlated with the extent of intellectual impairment as measured by a memory information test; muscarinic cholinergic receptor binding activity remained unchanged with increasing senile plaque formation but butyrylcholinesterase activity increased. The results suggest a close relation between changes in the cholinergic system and Alzheimer's dementia, but the precise role of the system in this disease remains to be elucidated.
Length of Time to be Studied in Dietary Nutritional Surveys (1978)

本研究によってえられた結果は, 以下のごとくまとめられる。1) 調査期間を延長することによってえられる集団の平均値の変動はどの栄養素でも小さくなる。2) その際, 栄養素によって変動の縮小に差があり, たとえばカルシウムは縮小が著しく, 変動係数は約1/10の大きさになるが, 脂質では, 約1/3になるにすぎない。3) 調査期間を7日にすることによって, 30日の記録からえられた集団の平均値とえられた平均値とのへだたりは小さくなる。4) 個人の1日あたり平均値を事前に作成し, それを用いて集団の平均値, 不偏分散をもとめ, 母平均の区間推定を行なってみると, その区間内に30日の集団の平均値が含まれる頻度はカルシウムで90%以上, エネルギーで80%前後, たん白質・鉄で60～70%であるが, 他の栄養素では50%に満たない。
Construction of a new open-framework solid from 1,3,5-cyclohexanetricarboxylate and zinc(II) building blocks (1997)

Addition copolymerization of cis,cis-1,3,5-cyclohexanetricarboxylate (CTC) with zinc(II) at 25 °C yielded the extended co-ordination solid, Zn 3 [(CTC)(C 5 H 5 N)] 2 · 2(CH 3 ) 2 NC(O)H, which has one-dimensional channels with an aperture of nearly 6 Å as found by an X-ray crystallographic study.
Prediction of the Formation and Stabilities of Energetic Salts and Ionic Liquids Based on ab Initio Electronic Structure Calculations (2005)

A computational approach to predict the thermodynamics for forming a variety of imidazolium-based salts and ionic liquids from typical starting materials is described. The gas-phase proton and methyl cation acidities of several protonating and methylating agents, as well as the proton and methyl cation affinities of many important methyl-, nitro-, and cyano-substituted imidazoles, have been calculated reliably by using the computationally feasible DFT (B3LYP) and MP2 (extrapolated to the complete basis set limit) methods. These accurately calculated proton and methyl cation affinities of neutrals and anions are used in conjunction with an empirical approach based on molecular volumes to estimate the lattice enthalpies and entropies of ionic liquids, organic solids, and organic liquids. These quantities were used to construct a thermodynamic cycle for salt formation to reliably predict the ability to synthesize a variety of salts including ones with potentially high energetic densities. An adjustment of the gas phase thermodynamic cycle to account for solid- and liquid-phase chemistries provides the best overall assessment of salt formation and stability. This has been applied to imidazoles (the cation to be formed) with alkyl, nitro, and cyano substituents. The proton and methyl cation donors studied were as follows: HCl, HBr, HI, (HO)2SO2, HSO3CF3 (TfOH), and HSO3(C6H4)CH3 (TsOH); CH3Cl, CH3Br, CH3I, (CH3O)2SO2, CH3SO3CF3 (TfOCH3), and CH3SO3(C6H4)CH3 (TsOCH3). As substitution of the cation with electron-withdrawing groups increases, the triflate reagents appear to be the best overall choice as protonating and methylating agents. Even stronger alkylating agents should be considered to enhance the chances of synthetic success. When using the enthalpies of reaction for the gas-phase reactants (eq 6) to form a salt, a cutoff value of -13 kcal mol(-1) or lower (more negative) should be used as the minimum value for predicting whether a salt can be synthesized.
Staphylococcus aureus β-toxin Production is Common in Strains With the β-toxin Gene Inactivated by Bacteriophage (2014)

This study demonstrates the dynamic interaction between S. aureus and the infected host, where φSa3 serves as a regulator of virulence gene expression, and increased fitness and virulence in new environments.
Evaluation of matrix metalloproteinases and serine proteases activities in three B16 melanoma cell lines with distinct tumorigenic potential. (1994)

Mouse B16 melanoma cells (B16, parental line) and two derived clones either pigmented (B16P) or non pigmented (B16NP) were cultured as monolayers (2D) or on agar, as aggregates (3D). The productions of gelatinases A and B (72 kDa and 92 kDa type IV collagenases) and their inhibitors (TIMP1 and TIMP2), plasminogen activators (PAs) and plasminogen activator inhibitors (PAI) were investigated. The B16 cell lines did not secrete any gelatinase, but they secreted TIMP2, tissue-type (t-PA), urokinase-type (u-PA) plasminogen activators and PAI-1 like activities. High levels of PAI activity were determined in conditioned media and cellular extracts of B16NP, which could account for the lower tumorigenic potential of these cells. In 3D cultures, the cellular extracts of the three cell lines contained essentially u-PA activity. This activity could contribute to the greater tumorigenic and invasive capacities of B16, B16P and B16NP when cultured in 3D.
The appearance of the feet in Pfeiffer syndrome caused by FGFR1 P252R mutation (2003)

Patients affected by Pfeiffer syndrome generally present with syndromic craniosynostosis and typical limb defects including broad thumbs, wide halluces with varus deformity, toe syndactyly and sometimes elbow ankylosis. This autosomal dominant condition can be caused by mutations in either fibroblast growth factor receptor gene type 1 or 2 (FGFR1 or FGFR2). We report four new affected families showing an FGFR1 P252R mutation and emphasize the characteristic malformations of the feet in this form of Pfeiffer syndrome. In one family this was the only abnormality.
Exploration in Interactive Personalized Music Recommendation: A Reinforcement Learning Approach (2013)

Current music recommender systems typically act in a greedy fashion by recommending songs with the highest user ratings. Greedy recommendation, however, is suboptimal over the long term: it does not actively gather information on user preferences and fails to recommend novel songs that are potentially interesting. A successful recommender system must balance the needs to explore user preferences and to exploit this information for recommendation. This paper presents a new approach to music recommendation by formulating this exploration-exploitation trade-off as a reinforcement learning task called the multi-armed bandit. To learn user preferences, it uses a Bayesian model, which accounts for both audio content and the novelty of recommendations. A piecewise-linear approximation to the model and a variational inference algorithm are employed to speed up Bayesian inference. One additional benefit of our approach is a single unified model for both music recommendation and playlist generation. Both simulation results and a user study indicate strong potential for the new approach.
Microfabricated Deposition Nozzles for Direct‐Write Assembly of Three‐Dimensional Periodic Structures (2005)

Direct-write assembly of a three- dimensional periodic structure comprised of hexagonal filaments is demonstated. The structure is created by robotically depositing a concentrated colloidal gel-based ink through a cylindrical deposition nozzle modified by attaching a UV-LIGA (lithography, electroplating, and molding)-fabricated hexagonal micro (μ)-tip that controls filament geometry.
Retinitis Pigmentosa GTPase Regulator (RPGR)-interacting Protein Is Stably Associated with the Photoreceptor Ciliary Axoneme and Anchors RPGR to the Connecting Cilium (2001)

Retinitis pigmentosa (RP) is a blinding retinal disease in which the photoreceptor cells degenerate. Mutations in the gene for retinitis pigmentosa GTPase regulator (RPGR) are a frequent cause of RP. The function of RPGR is not well understood, but it is thought to be a putative guanine nucleotide exchange factor for an unknown G protein. Ablation of the RPGR gene in mice suggested a role in maintaining the polarized distribution of opsin across the cilia. To investigate its function, we used a protein interaction screen to identify candidate proteins that may interact physiologically with RPGR. One such protein, designated RPGR-interacting protein (RPGRIP), is expressed specifically in rod and cone photoreceptors. It consists of an N-terminal region predicted to form coiled coil structures linked to a C-terminal tail that binds RPGR. In vivo, both proteins co-localize in the photoreceptor connecting cilia. RPGRIP is stably associated with the ciliary axoneme independent of RPGR and is resistant to extraction under conditions that partially solubilized other cytoskeletal components. When over-expressed in heterologous cell lines, RPGRIP appears in insoluble punctate and filamentous structures. These data suggest that RPGRIP is a structural component of the ciliary axoneme, and one of its functions is to anchor RPGR within the cilium. RPGRIP is the only protein known to localize specifically in the photoreceptor connecting cilium. As such, it is a candidate gene for human photoreceptor disease. The tissue-specific expression of RPGRIP explains why mutations in the ubiquitously expressed RPGR confer a photoreceptor-specific phenotype.
A role for decorin in cutaneous wound healing and angiogenesis (2006)

Decorin is known to influence tissue tensile strength and cellular phenotype. Therefore, decorin is likely to have an impact on tissue repair, including cutaneous wound healing. In this study, cutaneous healing of both excisional and incisional full-thickness dermal wounds was studied in decorin-deficient (Dcn(-/-)) animals. A statistically significant delay in excisional wound healing in the Dcn(-/-) mice occurred at 4 and 10 days postwounding and, in incisional wounds at 4, 10, and 18 days when compared with wild-type (Dcn(-/-)) controls. Fibrovascular invasion into polyvinylalcohol sponges was significantly increased by day 18 in Dcn(-/-) mice relative to Dcn(+/+) mice. The 18-day sponge implants in the Dcn(-/-) mice showed a marked accumulation of biglycan when compared with the corresponding implants in Dcn(+/+) mice. Thus, regulated production of decorin may serve as an excellent therapeutic approach for modifying impaired wound healing and harmful foreign body reactions.