gebhart/patrepeval huggingface dataset:
Metabolic Specialization of Mouse Embryonic Stem Cells (2012)

The cell doubling time of mouse embryonic stem (ES) cells is shorter than that of even the most aggressively growing cancer cells. To investigate whether mouse ES cells might exist in a unique metabolic state supportive of rapid growth, organic extracts were prepared and analyzed by mass spectrometry. Upon comparison of mouse ES cells with differentiating embryoid bodies, such assays revealed profound differences in the abundance of metabolites associated with one‐carbon metabolism. It was also noted that the abundance of both threonine and acetyl‐CoA changed markedly as ES cells differentiate into embryoid bodies. These differences in metabolite abundance were traced to the copious, ES cell‐specific expression of the gene encoding threonine dehydrogenase (TDH). TDH gene expression was observed to be 1,000‐fold higher in ES cells than any of 7 tissues assayed from adult mice. The TDH enzyme catalyzes the mitochondrial breakdown of threonine into glycine and acetyl‐CoA. Glycine is further catabolized by mitochondrial enzymes associated with the glycine cleavage system to foster the charging (methylation) of tetrahydrofolate, a key intermediate in purine synthesis. The acetyl‐CoA produced from TDH‐mediated breakdown of threonine can be fed into the TCA cycle, used as a building block for the synthesis of lipids and sterols, or deployed as a substrate for protein acetylation. This TDH‐dependent metabolic pathway is prototypic of rapidly growing microbial organisms, and is a component of what has been termed the high flux backbone of microbial metabolism. Nutritional, pharmacologic and genetic approaches have been used to confirm the unique dependency of mouse ES cells on threonine consumption as a metabolic fuel. This research was supported by a program project grant funded by The National Cancer Institute and philanthropic contributions from an anonymous donor.
First‐principles calculation and X‐ray absorption fine structure analysis of Fe doping mechanism for semi‐insulating GaN growth on GaAs substrates (2007)

Abstract In order to fabricate an Fe‐doped semi‐insulating (SI) GaN substrate by hydride vapor phase epitaxy (HVPE) using (111)A GaAs as a starting substrate, the Fe doping mechanism was investigated by two approaches: first‐principles calculation and X‐ray absorption fine structure (XAFS) measurements. First‐principles study clarified that Fe and As atoms are substituting for the Ga and N atoms in the wurtzite GaN lattice, respectively. In addition, incorporation of Fe in GaN was found to be hindered by adjacent As in the N site. XAFS analysis performed for an Fe‐doped SI GaN substrate, obtained by protecting backside of the GaAs substrate, showed that the Fe atoms are substituting for the Ga site in GaN. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Prevalence of anxiety and depression in people with different types of cancer or haematologic malignancies: a cross-sectional study (2022)

The prevalence of anxiety and depression is high in cancer patients. Type of cancer is an important predictor for anxiety and depressive symptoms, with lung and brain cancer patients being highly burdened. Considering a personalised medicine approach, physicians should take into account the high prevalence of psychiatric comorbidities and include psychiatric consultations in the treatment plan.
PO-296 Identification of novel players of tumour – macrophage crosstalk in lung cancer (2018)

Introduction Tumor-macrophage (Mφ) crosstalk has been extensively studied and both cytokine networks and cell-cell interactions at the tumour site directly impact therapeutic outcome. Tumour modelling brings up tools that can be explored to uncover targets for therapeutic intervention. We developed a model system based on the co-culture of lung tumour spheroids, fibroblasts and Mφ, which can emulate aspects of tumour microenvironment dynamics. In co-culture, Mφ infiltrate the tumour mass and display tumour promoting features, e.g. secretion of M2-like cytokines, among which CCL24 showed the highest upregulation. In a tumoral context, CCL24 was shown to be upregulated in primary tumours and liver metastasis of colorectal cancer and contributes to hepatocellular carcinoma malignancy. Therefore, this study aims to investigate this chemokine for its possible role in NSCLC invasion and metastasis. Material and methods Three lung cancer cell lines (NCI-H157, NCI-H1650, NCI-H1437), representing tumour stages with different invasion potential and EMT scores, and 3 sources of fibroblasts (cancer-associated – CAF, normal – NF, human dermal fibroblasts – hDF) were supplemented with increasing concentrations of CCL24. Gene expression of EMT markers, transwell invasion and EDU proliferation assays were performed. Results and discussions In the model, a tumor-supportive secretory profile was observed, with identification of cytokines associated with M2-like Mφ polarisation (G-CSF, IL4, IL13, IL10). Hierarchical clustering analysis identified CXCL13, CCL22, CCL23 and CCL24 as cytokines specifically upregulated in triple cultures. CCL24 supplementation resulted in an increase in the invasion potential of lung cancer cell lines (up to 40%), most evident in non-invasive cell line NCI-H1437. This was concomitant with an upregulation of EMT markers Slug and Snail (up to 5-fold) in NCI-H1437 cells. hDF showed a marked increase in the invasion potential (up to 2-fold), while for CAF and NF the increase was around 20%. No effects in proliferation were observed. Conclusion This data suggests that CCL24 promotes the invasion but not the proliferation of lung cancer cell lines, which could be linked to an EMT process in non-invasive cell lines presenting an epithelial phenotype. We are currently investigating the downstream effectors, namely upregulation of MMPs and angiogenesis stimulating factors. We acknowledge the IMI Joint Undertaking (grant agreement no.115188) and FCT (iNOVA4Health—UID/Multi/04462/2013, SFRH/BD/52202/2013).
[Visual impairment caused by recreational usage of cocaine--a case report]. (2010)

We presented a case of sudden and painless vision impairment connected with the recreational usage of cocaine. According to many authors illicit use of cocaine has been associated with the most common adverse effect among all psychoactive drugs. In the last years there were a few articles about vision problems after the usage of cocaine. In most cases the main mechanism was central retinal artery occlusion (CRAO). The vision impairment developed from 3 to 10 hrs after the cocaine use and the outcome, despite the intensive treatment, was usually poor. All doctors should keep in mind the possibility of cocaine usage, in young and healthy people, who developed a sudden and painless vision loss.
Computational Electromagnetics in Service of Polarimetric Phased Array Radar Calibration - What Causes the Differential Phase bias? (2018)

Calibration of the planar polarimetric phased array radar for weather purposes is angle dependent. Yet measuring of all parameters required to calibrate polarimetric variables is impractical for large radar antennas. Here, an alternative computational electromagnetic modeling approach is considered. We use a full size demonstrator of larger polarimetric radar for evaluation of polarimetric biases expected in the larger array. Particularly, we attempt identification of the bias sources in the differential phase measurements.
Identification, Molecular Cloning, and Analysis of Full-Length Hepatitis C Virus Transmitted/Founder Genotypes 1, 3, and 4 (2015)

Hepatitis C virus (HCV) infects 2% to 3% of the world's population and exhibits extraordinary genetic diversity. This diversity is mirrored by HIV-1, where characterization of transmitted/founder (T/F) genomes has been instrumental in studies of virus transmission, immunopathogenesis, and vaccine development. Here, we show that despite major differences in genome organization, replication strategy, and natural history, HCV (like HIV-1) diversifies essentially randomly early in infection, and as a consequence, sequences of actual T/F viruses can be identified. This allowed us to capture by molecular cloning the full-length HCV genomes that are responsible for infecting the first hepatocytes and eliciting the initial immune responses, weeks before these events could be directly analyzed in human subjects. These findings represent an enabling experimental strategy, not only for HCV and HIV-1 research, but also for other RNA viruses of medical importance, including West Nile, chikungunya, dengue, Venezuelan encephalitis, and Ebola viruses.
Structure and properties of segmented poly(ether‐ester)s, 7. Model triblock copolyesters of monodisperse block length (1983)

Abstract Synthesis and characterization of model triblock copolyesters, in which the two end‐blocks are based on tetramethylene terephthalate and the middle block is oligo(oxytetramethylene), are described. These model copolyesters, which are essentially monodisperse, and similarly prepared segmented block copolyesters with monodisperse blocks exhibit the same dependency of the melting temperature on the degree of polymerization of the ester blocks as polydisperse technical copoly(ether‐ester)s.
Interest of MIA in frequency domain? (2015)

Mutual Information Analysis (MIA) has a main advantage over Pearson's correlation Analysis (CPA): its ability in detecting any kind of leakage within traces. However, it remains rarely used and less popular than CPA; probably because of two reasons. The first one is related to the appropriate choice of hyperparameters involved in MIA, choice that determines its efficiency and genericity. The second one is surely the high computational burden associated to MIA. The interests of applying MIA in the frequency domain rather than in the time domain are discussed. It is shown that MIA running into the frequency domain is really effective and fast when combined with the use of an accurate frequency leakage model.
ChemInform Abstract: Apoptolidines E (I) and F (II), New Glycosylated Macrolactones Isolated from Nocardiopsis sp. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Differentiating Double-Layer, Pseudocapacitance, and Battery-like Mechanisms by Analyzing Impedance Measurements in Three Dimensions (2020)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionDifferentiating Double-Layer, Pseudocapacitance, and Battery-like Mechanisms by Analyzing Impedance Measurements in Three DimensionsJesse S. Ko*Jesse S. KoStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States*Email: [email protected]More by Jesse S. Ko, Chun-Han LaiChun-Han LaiUniversity of California, Los Angeles, Materials Science & Engineering, Los Angeles, California 90095, United StatesMore by Chun-Han Lai, Jeffrey W. LongJeffrey W. LongU.S. Naval Research Laboratory, Chemistry Division (Code 6170), Washington, DC, 20375, United StatesMore by Jeffrey W. Longhttp://orcid.org/0000-0002-5184-5260, Debra R. RolisonDebra R. RolisonU.S. Naval Research Laboratory, Chemistry Division (Code 6170), Washington, DC, 20375, United StatesMore by Debra R. Rolison, Bruce DunnBruce DunnUniversity of California, Los Angeles, Materials Science & Engineering, Los Angeles, California 90095, United StatesMore by Bruce Dunnhttp://orcid.org/0000-0001-5669-4740, and Johanna Nelson Weker*Johanna Nelson WekerStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States*Email: [email protected]More by Johanna Nelson Wekerhttp://orcid.org/0000-0001-6856-3203Cite this: ACS Appl. Mater. Interfaces 2020, 12, 17, 20145Publication Date (Web):April 14, 2020Publication History Published online14 April 2020Published inissue 29 April 2020https://pubs.acs.org/doi/10.1021/acsami.0c05507https://doi.org/10.1021/acsami.0c05507correctionACS PublicationsCopyright © 2020 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1443Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (543 KB) Get e-Alertsclose Get e-Alerts
Reduced complexity control design for symmetric LPV systems (2015)

We use symmetry to reduce the computational complexity of designing parameter-dependent controllers and Lyapunov functions. We propose three complementary methods for exploiting symmetry to reduce the complexity. The first method uses symmetry to reduce the number of design variables. The second method uses symmetry to reduce the dimension of the design variables. And the third method reduces the number of linear matrix inequalities that the design variables must satisfy. We apply our reduced complexity control design to a building control problem. We show that, for this example, our method leads to an exponential decrease in the number of design variables and linear matrix inequalities.
Supplementary Figure 1 from <i>HOXB13</i> G84E Mutation in Finland: Population-Based Analysis of Prostate, Breast, and Colorectal Cancer Risk (2023)

&lt;p&gt;PDF file - 90K, The first row shows the amino acid sequence. In the second row the predicted secondary structure is illustrated with blue (coil), red (alpha-helix) and green (beta-strand) bars. In the third row numerical value for the confidence of the prediction of secondary structure is indicated by a value ranging from 0-9. The confidence value of zero indicates the lowest possible confidence of prediction while 9 is represents the highest value of confidence. The values in the fourth row represents the relative solvent accessibility. Zero indicates a 0-9% relative solvent accessibility while the value of 9 indicates 90-100% solvent accessibility. The fifth row indicates the confidence value for the prediction of relative solvent accessibility ranging from 0-9. The confidence value of zero indicates the lowest possible confidence of prediction while 9 is represents the highest value of confidence.&lt;/p&gt;
Synthesis and characterization of new biologically active 2‐(1,3‐disubstituted pyrazolyl)chromones and corresponding pyrimidine, thiopyrimidine, pyrazolyl derivatives (2004)

Abstract A series of 2‐(1‐methyl‐3‐ n ‐propylpyrazol‐5‐yl)‐chromones with interesting Phosphodiesterase IV inhibitition activities were synthesized. Different derivatives of the titled compounds like aminopyrimidine, thiopyrimidine, pyrazolyl were synthesized and their Phosphodiesterase IV inhibitition activities were checked.
Fast source independent estimation of lithographic difficulty supporting large scale source optimization (2012)

Many chip design and manufacturing applications including design rules development, optical proximity correction tuning, and source optimization can benefit from rapid estimation of relative difficulty or printability. Simultaneous source optimization of thousands of clips has been demonstrated recently, but presents performance challenges. We describe a fast, source independent method to identify patterns which are likely to dominate the solution. In the context of source optimization the estimator may be used as a filter after clustering, or to influence the selection of representative cluster elements. A weighted heuristic formula identifies spectral signatures of several factors contributing to difficulty. Validation methods are described showing improved process window and reduced error counts on 22 nm layout compared with programmable illuminator sources derived from hand picked patterns, when the formula is used to influence training clip selection in source optimization. We also show good correlation with fail prediction on a source produced with hand picked training clips with some level of optical proximity correction tuning.
Speculative Buffer Overflows: Attacks and Defenses (2018)

Practical attacks that exploit speculative execution can leak confidential information via microarchitectural side channels. The recently-demonstrated Spectre attacks leverage speculative loads which circumvent access checks to read memory-resident secrets, transmitting them to an attacker using cache timing or other covert communication channels. We introduce Spectre1.1, a new Spectre-v1 variant that leverages speculative stores to create speculative buffer overflows. Much like classic buffer overflows, speculative out-of-bounds stores can modify data and code pointers. Data-value attacks can bypass some Spectre-v1 mitigations, either directly or by redirecting control flow. Control-flow attacks enable arbitrary speculative code execution, which can bypass fence instructions and all other software mitigations for previous speculative-execution attacks. It is easy to construct return-oriented-programming (ROP) gadgets that can be used to build alternative attack payloads. We also present Spectre1.2: on CPUs that do not enforce read/write protections, speculative stores can overwrite read-only data and code pointers to breach sandboxes. We highlight new risks posed by these vulnerabilities, discuss possible software mitigations, and sketch microarchitectural mechanisms that could serve as hardware defenses. We have not yet evaluated the performance impact of our proposed software and hardware mitigations. We describe the salient vulnerability features and additional hypothetical attack scenarios only to the detail necessary to guide hardware and software vendors in threat analysis and mitigations. We advise users to refer to more user-friendly vendor recommendations for mitigations against speculative buffer overflows or available patches.
Understanding Mobile App Reviews to Guide Misuse Audits (2023)

Problem: We address the challenge in responsible computing where an exploitable mobile app is misused by one app user (an abuser) against another user or bystander (victim). We introduce the idea of a misuse audit of apps as a way of determining if they are exploitable without access to their implementation. Method: We leverage app reviews to identify exploitable apps and their functionalities that enable misuse. First, we build a computational model to identify alarming reviews (which report misuse). Second, using the model, we identify exploitable apps and their functionalities. Third, we validate them through manual inspection of reviews. Findings: Stories by abusers and victims mostly focus on past misuses, whereas stories by third parties mostly identify stories indicating the potential for misuse. Surprisingly, positive reviews by abusers, which exhibit language with high dominance, also reveal misuses. In total, we confirmed 156 exploitable apps facilitating the misuse. Based on our qualitative analysis, we found exploitable apps exhibiting four types of exploitable functionalities. Implications: Our method can help identify exploitable apps and their functionalities, facilitating misuse audits of a large pool of apps.
Few Shot Dialogue State Tracking using Meta-learning (2021)

Saket Dingliwal, Shuyang Gao, Sanchit Agarwal, Chien-Wei Lin, Tagyoung Chung, Dilek Hakkani-Tur. Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume. 2021.
Abstract 661: Tie2 Deficiency Leads to Lymphatic Defects and Resistance to High-fat Diet Induced Obesity (2015)

The Angiopoietin-Tie2 signaling pathway is a critical regulator in vascular development, with conventional Ang1 or Tie2 knockout mice dying in utero with vascular defects. While the role of this pathway in vascular development is apparent, the severity of developmental phenotypes makes it difficult to study Tie2 in vivo. Here, we investigate the functional role of Tie2 in embryonic as well as adult mice using inducible knockout mouse models (Tie2 cKO). Tie2 inactivation at early stages of gestation (E12.5 or E14.5), which coincides with the initial stages of lymphatic development and remodeling, resulted in severe subcutaneous edema in E16.5 and altered lymphatic vessel morphology in the dermis of E17.5. These results indicate the important role of Tie2 in lymphatic development. In contrast, Tie2 inactivation at later stages (E18.5-P0) resulted in the birth of viable pups, indicating that Tie2 is dispensable after embryonic development. Adult male Tie2 cKO mice have similar blood glucose, glucose tolerance, and plasma lipids compared to controls. However, body weight of Tie2 cKO mice upon high-fat diet feeding was lower than that of control mice (47.5+-0.6g (control) vs. 38.0+-2.0g (Tie2 cKO), p&lt;0.01 (4weeks after high-fat diet feeding)). Although plasma lipids (cholesterol and triglyceride) in control and Tie2 cKO mice were similar after high-fat diet feeding, mRNA expression of TNFa (100+-14% (control) vs. 40+-1.4% (Tie2 cKO), p&lt;0.05) and F4/80 (100+-13% (control) vs. 53+-7.3% (Tie2 cKO), p&lt;0.05) in epididymal fat were reduced in Tie2 cKO mice. Our data show that Tie2 plays an import role in lymphatic development during embryogenesis and that Tie2 signaling is also important for adipose tissue growth in adult mice.
An Efficient Auction-based Mechanism for Mobile Data Offloading (2014)

The opportunistic utilization of third party WiFi access devices to offload customer traffic from the mobile network has recently gained momentum as a promising approach to increase the network capacity and simultaneously reduce the energy consumption of the radio access network (RAN) infrastructure. To foster the opportunistic utilization of unexploited Internet connections, we propose a new and open market where a mobile operator can lease the bandwidth made available by third parties (residential users or private companies) through their access points to increase dynamically (and adaptively) the network capacity. We formulate the offloading problem as a reverse auction considering the most general case of partial covering of the traffic to be offloaded. We discuss the conditions (i) to offload the maximum amount of data traffic according to the capacity made available by third party access devices, (ii) to foster the participation of access point owners (individual rationality), and (iii) to prevent market manipulation (incentive compatibility). Finally, we propose three alternative greedy algorithms that efficiently solve the offloading problem, even for large-size network scenarios.