gebhart/patrepeval huggingface dataset:
Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing (2008)

Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is organized around a maternally methylated CpG island comprising the promoters of the adjacent PEG10 and SGCE imprinted genes. Examination of Dnmt3l(-/+) conceptuses shows that imprinted expression for all genes of the cluster depends upon the germline methylation at this putative "imprinting control region" (ICR). Similarly as for other ICRs, we find its DNA-methylated allele to be associated with trimethylation of lysine 9 on histone H3 (H3K9me3) and trimethylation of lysine 20 on histone H4 (H4K20me3), whereas the transcriptionally active paternal allele is enriched in H3K4me2 and H3K9 acetylation. Our study reveals a novel placenta-specific transcript, TFPI2, which is expressed from the maternal allele in both humans and mice. Deficiency for the histone methyltransferase EHMT2 (also known as G9A) or for the Polycomb group protein EED, involved in repressive H3K9me2 and H3K27me3 respectively, leads to biallelic expression of Tfpi2 in the extra-embryonic lineages, whereas the other genes in the cluster maintain correct imprinting. Apart from the putative ICR, however, no other promoter regions within the domain exhibited allele-specific repressive histone modifications. This unexpected general lack of repressive histone modifications suggests that this domain may utilize a different silencing mechanism as compared to other imprinted domains.
Biofunctionalized Plants as Diverse Biomaterials for Human Cell Culture (2017)

The commercial success of tissue engineering products requires efficacy, cost effectiveness, and the possibility of scaleup. Advances in tissue engineering require increased sophistication in the design of biomaterials, often challenging the current manufacturing techniques. Interestingly, several of the properties that are desirable for biomaterial design are embodied in the structure and function of plants. This study demonstrates that decellularized plant tissues can be used as adaptable scaffolds for culture of human cells. With simple biofunctionalization technique, it is possible to enable adhesion of human cells on a diverse set of plant tissues. The elevated hydrophilicity and excellent water transport abilities of plant tissues allow cell expansion over prolonged periods of culture. Moreover, cells are able to conform to the microstructure of the plant frameworks, resulting in cell alignment and pattern registration. In conclusion, the current study shows that it is feasible to use plant tissues as an alternative feedstock of scaffolds for mammalian cells.
MR‐guided placement of a temporary vena cava filter: Technique and feasibility (1998)

The purpose of this paper was to investigate the feasibility of MR-guided insertion of a temporary vena cava filter on an open low-field imager. In vivo procedures were performed on four anesthetized pigs using a common nonferromagnetic temporary vena cava filter and a special prototype guidewire developed for vascular interventions guided by low-field MRI. Breath-hold spoiled gradient-echo sequences (fast low-angle shot [FLASH]) with flow compensation were used for position monitoring of the passively visualized intravascular devices. Using the described technique and equipment, all steps of the procedure were feasible in the MR unit. Practicability of the procedure seems to be sufficient for clinical purposes but was inferior compared to the conventional technique of filter placement.
Live demonstration: The &#x201C;DAVIS&#x201D; Dynamic and Active-Pixel Vision Sensor (2014)

This demonstration will show the features of the Dynamic and Active-Pixel Vision Sensor (DAVIS) reported at the VLSI Symposium and the International Imager Sensor Workshop in 2013. This sensor concurrently outputs conventional CMOS image sensor frames and sparse, low-latency dynamic vision sensor events from the same pixels, sharing the same photodiodes. The setup will allow visitors to explore the advantages of combining of fast and computationally-efficient neuromorphic event-driven vision with the existing body of methods for frame-based computer and machine vision.
Rapid Phenotypic Antibiotic Susceptibility Testing Through RNA Detection (2017)

Abstract Background Culture-based antibiotic susceptibility testing, the gold standard, is too slow to guide early antibiotic selection, while newer genotypic methods require comprehensive knowledge of resistance mechanisms to predict phenotype. Quantitative measurement of key antibiotic-responsive transcripts offers a rapid, phenotypic assay for assessing antibiotic susceptibility, agnostic to the genetic basis for resistance. Methods We performed RNA-Seq on Klebsiella pneumoniae and Acinetobacter baumanii treated with ciprofloxacin, gentamicin, or meropenem for 0, 10, 30, and 60 minutes. For each, we identified 50 responsive transcripts whose expression levels differ most between susceptible and resistant organisms upon antibiotic exposure. We measured their expression using a multiplexed fluorescent RNA hybridization assay (NanoString) in 69 clinical isolates, including a “test set” of multidrug-resistant strains from the CDC, in an 8-hour assay. Gene expression data from test strains were compared against known susceptible and resistant isolates to generate a transcriptional susceptibility metric. We also designed NanoString probes to detect 5 carbapenemase genes (KPC-2, KPC-3, NDM-1, OXA-48, and CTX-M15). Results Across all bacteria-antibiotic pairs tested, a susceptibility metric derived from these transcriptional assays correctly grouped isolates in 167 of 173 tests (Table 1), with only 1 of 88 resistant isolates misclassified as susceptible. Five of six incorrectly grouped isolates were within one dilution of the breakpoint MIC, including the misclassified resistant isolate. Conclusion We demonstrate phenotypic antibiotic resistance detection based on fluorescent RNA detection in an 8-hour assay. We have previously published proof-of-concept studies that this assay may be run on a positive blood culture bottle with minimal sample processing. By coupling this phenotypic assay with detection of genetic resistance determinants (demonstrated for carbapenemases) in a single assay, strains with unexplained resistance can be prioritized for further study. Disclosures All authors: No reported disclosures.
Cloning and expression of a family of inward rectifier potassium channels. (1994)

Five new members of the two-transmembrane domain potassium channel family have been identified from rat brain, heart and skeletal muscle. The channel mRNAs are differentially expressed and found in both the central nervous system and periphery. Expression of two of these channels in Xenopus oocytes gave rise to inwardly rectifying potassium currents which were voltage-dependently blocked by barium and cesium. Voltage command pulses negative to Ek evoked inward currents which rapidly reached a peak amplitude and relaxed to a steady-state level. The quantity of current relaxation differed in the two channels and was increased at more negative potentials. The degree of current rectification was also different for the two channels. The results demonstrate the existence of a large and widely expressed family of inward rectifier potassium channel subunits with distinct tissue distributions and functional properties.
Mutations in ionotropic AMPA receptor 3 alter channel properties and are associated with moderate cognitive impairment in humans (2007)

Ionotropic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (iGluRs) mediate the majority of excitatory synaptic transmission in the CNS and are essential for the induction and maintenance of long-term potentiation and long-term depression, two cellular models of learning and memory. We identified a genomic deletion (0.4 Mb) involving the entire GRIA3 (encoding iGluR3) by using an X-array comparative genomic hybridization (CGH) and four missense variants (G833R, M706T, R631S, and R450Q) in functional domains of iGluR3 by sequencing 400 males with X-linked mental retardation (XLMR). Three variants were found in males with moderate MR and were absent in 500 control males. Expression studies in HEK293 cells showed that G833R resulted in a 78% reduction of iGluR3 due to protein misfolding. Whole-cell recording studies of iGluR3 homomers in HEK293 cells revealed that neither iGluR3-M706T (S2 domain) nor iGluR3-R631S (near channel core) had substantial channel function, whereas R450Q (S1 domain) was associated with accelerated receptor desensitization. When forming heteromeric receptors with iGluR2 in HEK293 cells, all four iGluR3 variants had altered desensitization kinetics. Our study provides the genetic and functional evidence that mutant iGluR3 with altered kinetic properties is associated with moderate cognitive impairment in humans.
A Model for Metricising Privacy and Legal Compliance (2018)

In order for a dataset to be legally compliant - in some sense - with privacy laws such as the General Data Protection Regulation (GDPR) various steps must be taken to ensure the removal of data that might compromise or reveal personal data. This can be achieved through a process of removal of information content or semantics; which if done incorrectly can render that dataset in violation of such laws. Machine learning presents a technology based around the analysis of dependencies and correlations of a dataset. This can be used to measure information content within the bounds of the dependencies estimators used. Utilising this we can measure the effects of anonymisation upon a dataset and the efficacy of said anonymisation functions. If we additionally characterise what anonymisation means in terms of information loss and construct classification functions we have a framework in which the decision over whether an anonymisation is sufficient can be made. This can then be extended to an automation scenario where it becomes potentially possible that texts such as as the GDPR can be rendered as said classification functions.
Degradation mechanism of electrode tip during alternate resistance spot welding of zinc coated and uncoated steel sheets (2010)

The operation life and degradation mechanism of electrode during resistance spot alternating current welding of zinc coated galvannealed steel sheets were investigated. The electrode life in alternate resistance spot welding of zinc coated and uncoated steel sheets was extremely short in comparison with welding only on zinc coated steel sheets. During alternate resistance spot welding, the ring shaped nuggets were formed easily. This is attributable to the sticking of the alloy layers formed on the electrode top during the previous welding of zinc coated steel, to the uncoated steel surface at the following welding, so that notable wear took place, and the surface profile of electrode tip became flat. Additionally, an accumulation of highly resistant carbonaceous substance layer at the centre of electrode top caused an annular flow of welding current to hinder the nugget formation.
Phylogenetic Considerations in Designing a Broadly Protective Multimeric L2 Vaccine (2013)

While the oncogenic human papillomavirus (HPV) types with the greatest medical impact are clustered within the α9 and α7 species, a significant fraction of cervical cancers are caused by α5, α6, and α11 viruses. Benign genital warts are caused principally by the α10 viruses HPV6 and HPV11. In an effort to achieve broad protection against both cervical cancer- and genital wart-associated types, we produced at high levels in bacteria a multimeric protein (α11-88x8) fusing eight polypeptides corresponding to a protective domain comprising L2 residues ∼11 to 88 derived from HPV6 (α10), HPV16 (α9), HPV18 (α7), HPV31 (α9), HPV39 (α7), HPV51 (α5), HPV56 (α6), and HPV73 (α11) and a truncated derivative with the last three units deleted (α11-88x5). Mice were immunized three times with α11-88x8 or α11-88x5 adjuvanted with alum or the licensed HPV vaccines and challenged intravaginally with HPV6, HPV16, HPV26, HPV31, HPV33, HPV35, HPV45, HPV51, HPV56, HPV58, or HPV59 pseudovirions. The α11-88x5 and α11-88x8 vaccines induced similarly robust protection against each HPV type tested and indistinguishable HPV16-neutralizing antibody titers. Passive transfer of α11-88x8 antisera was protective. Further, rabbit antisera to α11-88x8 and α11-88x5 similarly neutralized native HPV18 virions. These findings suggest that immunologic competition between units is not a significant issue and that it is not necessary to include a unit of L2 derived from each species to achieve broader protection against diverse medically significant HPV types than is achieved with the licensed HPV vaccines.
Design, Analysis, Fabrication and Test of an Aspirated Fan Stage (2000)

A fan stage designed by means of a MISES-based quasi-3D approach (Youngren and Drela, 1991), for a pressure ratio of 1.6 at a tip Mach number of 0.7, has been analyzed by viscous 3D CFD, fabricated and tested in the MIT Blowdown Compressor. The design incorporates a rotor tip shroud and boundary layer removal on the suction surfaces of the rotor and stator and at other critical locations. The fully viscous 3D analysis enabled final detailing of the design. In tests, the stage has met its design objectives, producing the design pressure ratio of 1.6 at design speed. The mass flow removed totaled 4.7%, approximately 1.0% through slots on the suction surface of the rotor and stator, and the remainder distributed over the rotor shroud and stator hub. The measured adiabatic efficiency of the rotor for the throughflow was 96% at the design point and that for the stage was 90%. This paper presents the design, the results of the analysis and the experimental stage performance both at design and at some off-design conditions.
Increased prostaglandin-D 2 in male but not female STAT3-deficient hearts shifts cardiac progenitor cells from endothelial to white adipocyte differentiation (2020)

Abstract Cardiac levels of the signal transducer and activator of transcription factor-3 (STAT3) decline with age, and male but not female mice with a cardiomyocyte-specific STAT3 deficiency (CKO) display premature age-related heart failure associated with reduced cardiac capillary density. In the present study isolated male and female CKO-cardiomyocytes exhibit increased prostaglandin (PG)-generating cyclooxygenase-2 (COX-2) expression. The PG-degrading hydroxyprostaglandin-dehydrogenase-15 (HPGD) expression is only reduced in male cardiomyocytes, which is associated with increased PGD 2 secretion from isolated male but not female CKO-cardiomyocytes. Reduced HPGD expression in male cardiomyocytes derive from impaired androgen-receptor-(AR)-signaling due to loss of its co-factor STAT3. Elevated PGD 2 secretion in males is associated with increased white adipocyte accumulation in aged male but not female hearts. Adipocyte differentiation is enhanced in isolated SCA-1 + -cardiac-progenitor-cells (CPC) from young male CKO-mice compared to the adipocyte differentiation of male wildtype (WT)-CPC and CPC isolated from female mice. Epigenetic analysis in freshly isolated male CKO-CPC display hypermethylation in pro-angiogenic genes ( Fgfr2 , Epas1 ) and hypomethylation in the white adipocyte differentiation gene Zfp423 associated with upregulated ZFP423 expression and a shift from endothelial to white adipocyte differentiation compared to WT-CPC. The expression of the histone-methyltransferase EZH2 is reduced in male CKO-CPC compared to male WT-CPC whereas no differences in the EZH2 expression in female CPC were observed. Clonally expanded CPC can differentiate into endothelial cells or into adipocytes depending on the differentiation conditions. ZFP423 overexpression is sufficient to induce white adipocyte differentiation of clonal CPC. In isolated WT-CPC, PGD 2 stimulation reduces the expression of EZH2 thereby upregulating ZFP423 expression and promoting white adipocyte differentiation. Thus, cardiomyocyte STAT3-deficiency leads to age-related and sex-specific cardiac remodeling and failure in part due to sex-specific alterations in PGD 2 secretion and subsequent epigenetic impairment of the differentiation potential of CPC. Causally involved is the impaired AR signaling in absence of STAT3, which reduces the expression of the PG degrading enzyme HPGD.
Functional Kir7.1 channels localized at the root of apical processes in rat retinal pigment epithelium (2001)

1. The inwardly rectifying K+ channel current (IK(IR)) recorded from isolated retinal pigmented epithelial (RPE) cells showed poor dependence on external K+ ([K+]o) and low sensitivity to block by Ba2+. We examined the molecular identity and specific subcellular localization of the KIR channel in RPE cells. 2. The Kir7.1 channel current heterologously expressed in HEK293T cells (human embryonic kidney cell line) showed identical properties to those of the RPE IK(IR), i.e. poor dependence on [K+]o and low sensitivity to Ba2+ block. 3. Expression of Kir7.1 mRNA and protein was detected in RPE cells by RT-PCR and immunoblot techniques, respectively. 4. Immunohistochemical studies including electron microscopy revealed that the Kir7.1 channel was localized specifically at the proximal roots of the apical processes of RPE cells, where Na+,K+-ATPase immunoreactivity was also detected. 5. The middle-distal portions of apical processes of RPE cells in the intact tissue exhibited immunoreactivity of Kir4.1, a common KIR channel. In the isolated RPE cells, however, Kir4.1 immunoreactivity was largely lost, while Kir7.1 immunoreactivity remained. 6. These data indicate that the only IK(IR) recorded in isolated RPE cells is derived from the functional Kir7.1 channel localized at the root of apical processes. Co-localization with Na+,K+-ATPase suggests that the Kir7.1 channel may provide the pathway for recycling of K+ to maintain pump activity and thus is essential for K+ handling in RPE cells.
Crowdsourcing with multi-dimensional trust and active learning (2017)

We consider a typical crowdsourcing task that aggregates input from multiple workers as a problem in information fusion. To cope with the issue of noisy and sometimes malicious input from users, trust is used to model workers expertise. We propose a probabilistic model to jointly infer multi-dimensional trust of workers, multi-domain properties of questions, and true labels of questions. Our model is flexible and extensible to incorporate metadata associated with questions. To show that, we further propose two extended models, one of which handles input tasks with real-valued features and the other handles tasks with text features by incorporating topic models. In order to decrease entropies and reduce error rates more quickly with fewer annotations from workers, we further propose strategies for selecting which questions to ask and which workers to assign the questions to based on multidimension characteristics of questions and workers trust values in those dimensions. We evaluate our models and algorithms on real-world data sets. These results can be applied for fusion of information from multiple data sources like sensors, human input, machine learning results, or a hybrid of them.
Optimization-Intensive Watermarking Techniques for Decision Problems (2004)

Recently, a number of watermarking-based intellectual property protection techniques have been proposed. Although they have been applied to different stages in the design process and have a great variety of technical and theoretical features, all of them share two common properties: 1) they are applied solely to optimization problems and 2) do not involve any optimization during the watermarking process. In this paper, we propose the first set of optimization-intensive watermarking techniques for decision problems. In particular, we demonstrate, by example of the Boolean satisfiability (SAT) problem, how one can select a subset of superimposed watermarking constraints so that the uniqueness of the signature and the likelihood of satisfying the satisfiability problem are simultaneously maximized. We have developed three SAT watermarking techniques: adding clauses, deleting literals, and push-out and pull-back. Each technique targets different types of signature-induced constraint superimposition on an instance of SAT problem. In addition to comprehensive experimental validation, we theoretically analyze the potentials and limitations of the proposed watermarking techniques. Furthermore, we analyze the three proposed optimization-intensive watermarking SAT techniques in terms of their suitability for copy detection.
Joint Modeling of Local and Global Temporal Dynamics for Multivariate Time Series Forecasting with Missing Values (2020)

Multivariate time series (MTS) forecasting is widely used in various domains, such as meteorology and traffic. Due to limitations on data collection, transmission, and storage, real-world MTS data usually contains missing values, making it infeasible to apply existing MTS forecasting models such as linear regression and recurrent neural networks. Though many efforts have been devoted to this problem, most of them solely rely on local dependencies for imputing missing values, which ignores global temporal dynamics. Local dependencies/patterns would become less useful when the missing ratio is high, or the data have consecutive missing values; while exploring global patterns can alleviate such problem. Thus, jointly modeling local and global temporal dynamics is very promising for MTS forecasting with missing values. However, work in this direction is rather limited. Therefore, we study a novel problem of MTS forecasting with missing values by jointly exploring local and global temporal dynamics. We propose a new framework øurs, which leverages memory network to explore global patterns given estimations from local perspectives. We further introduce adversarial training to enhance the modeling of global temporal distribution. Experimental results on real-world datasets show the effectiveness of øurs for MTS forecasting with missing values and its robustness under various missing ratios.
SPRITE: A Response Model For Multiple Choice Testing (2015)

Item response theory (IRT) models for categorical response data are widely used in the analysis of educational data, computerized adaptive testing, and psychological surveys. However, most IRT models rely on both the assumption that categories are strictly ordered and the assumption that this ordering is known a priori. These assumptions are impractical in many real-world scenarios, such as multiple-choice exams where the levels of incorrectness for the distractor categories are often unknown. While a number of results exist on IRT models for unordered categorical data, they tend to have restrictive modeling assumptions that lead to poor data fitting performance in practice. Furthermore, existing unordered categorical models have parameters that are difficult to interpret. In this work, we propose a novel methodology for unordered categorical IRT that we call SPRITE (short for stochastic polytomous response item model) that: (i) analyzes both ordered and unordered categories, (ii) offers interpretable outputs, and (iii) provides improved data fitting compared to existing models. We compare SPRITE to existing item response models and demonstrate its efficacy on both synthetic and real-world educational datasets.