gebhart/patrepeval huggingface dataset:
Gravitationally induced phase shift on a single photon (2017)

The effect of the Earth's gravitational potential on a quantum wave function has only been observed for massive particles. In this paper we present a scheme to measure a gravitationally induced phase shift on a single photon travelling in a coherent superposition along different paths of an optical fiber interferometer. To create a measurable signal for the interaction between the static gravitational potential and the wave function of the photon, we propose a variant of a conventional Mach-Zehnder interferometer. We show that the predicted relative phase difference of $10^{-5}$ radians is measurable even in the presence of fiber noise, provided additional stabilization techniques are implemented for each arm of a large-scale fiber interferometer. Effects arising from the rotation of the Earth and the material properties of the fibers are analysed. We conclude that optical fiber interferometry is a feasible way to measure the gravitationally induced phase shift on a single-photon wave function, and thus provides a means to corroborate the equivalence of the energy of the photon and its effective gravitational mass.
Brillouin zone spin filtering mechanism of enhanced tunneling magnetoresistance and correlation effects in aCo(0001)/h -BN/Co(0001)magnetic tunnel junction (2015)

The Brillouin zone spin filtering mechanism of enhanced tunneling magnetoresistance (TMR) is described for magnetic tunnel junctions (MTJs) and studied for an example of the MTJ with hcp Co electrodes and hexagonal BN $(h$-BN) spacer. Our calculations based on the local density approximation of density-functional theory (LDA-DFT) for $\text{Co}(0001)/h\text{-BN}/\text{Co}(0001)$ MTJ predict high TMR in this device due to Brillouin zone filtering mechanism. Owning to the specific complex band structure of the $h$-BN the spin-dependent tunneling conductance of the system is ultrasensitive to small variations of the Fermi energy position inside the BN band gap. Doping of the BN and, consequentially, changing the Fermi energy position could lead to variation of the TMR by several orders of magnitude. We show also that taking into account correlation effects on beyond DFT level is required to accurately describe position of the Fermi level and thus transport properties of the system. Our study suggests that new MTJ based on hcp Co-Pt or Co-Pd disordered alloy electrodes and $p$-doped hexagonal BN spacer is a promising candidate for the spin-transfer torque magnetoresistive random-access memory.
Supplementary Table 7 - 8 from Identification of Campath-1 (CD52) as Novel Drug Target in Neoplastic Stem Cells in 5q-Patients with MDS and AML (2023)

&lt;p&gt;PDF file - 88K, Supplementary Table S7: Expression of the surface antigen CD52 on CD34+/CD38− cells and CD34+/CD38+ cells in CML, CMML, MDS/MPN-U, MPN, AUL, and ALL Supplementary Table S8: Expression of CD52 on CD34+/CD38− cells, CD34+/CD38+ cells, monocytes, and blood basophils in patients with ICUS, normal/reactive bone marrow, and complete long-term remission after AML.&lt;/p&gt;
Efficient production of novel floral traits in torenia by collective transformation with chimeric repressors of Arabidopsis transcription factors (2011)

Molecular breeding with genetic modification enables the production of novel floral traits in floricultural plants that could not be obtained by traditional breeding. To facilitate novel flower production, we collectively introduced 2 sets of 42 and 50 chimeric repressors of Arabidopsis transcription factors into Agrobacterium and then used these to co-transform torenia (Torenia fournieri). We generated 750 transgenic torenias, and identification of the transgenes revealed that more than 80% of the transgenic torenias had a single transgene. A total of 264 plants showed phenotypic modification, and 91.2% displayed modified flower colors and/or shapes, such as altered color patterns, curled petal margins, and wavy petals. These results indicated that the collective transformation system can be applied to molecular breeding of flowers. Detailed analysis of the phenotypes revealed that PETAL LOSS could control blotch sizes and that modification of cell shape could change the texture of petals. We found that the chimeric repressors of functionally unknown transcription factors also induced novel floral traits, and therefore, the transgenic torenias provide an understanding of the functions of transcription factors that could not be revealed by previous studies in Arabidopsis.
C-THAN: A new research center for the development of point-of-care technology for HIV/AIDS (2019)

The Center for Innovation in Point-of-Care Technologies for HIV/AIDS at Northwestern University (C-THAN) is a partner in the Point-of-Care Technologies Research Network (POCTRN) of the National Institutes of Biomedical Imaging and Bioengineering. POCTRN's mission is to drive the development of appropriate point-of-care (POC) diagnostic technologies through collaboration that merges scientific and technological capabilities with clinical need. C-THAN develops POC technologies for improved management of HIV/AIDS in low- and middle-income countries with a focus on sub-Saharan Africa. C-THAN incorporates clinical and user needs with technology expertise and resources to address commercialization and implementation barriers through: 1) assessment of unmet clinical needs in POC testing for HIV/AIDS and its comorbidities; 2) collaborations with physicians, researchers and engineers; 3) development of technical, clinical, industrial and regulatory partnerships; 4) clinical testing of prototype devices; and 5) creation of training opportunities for technology developers, evaluators, and other stakeholders. Technologies supported include tests for detection and monitoring of HIV/AIDS and its common comorbidities including tuberculosis, non-tuberculous mycobacteria, viral hepatitis and HIV-related malignancies. CTHAN relies on collaborations established by Northwestern University in Nigeria, South Africa, Mali and Tanzania, to have impact on the prevention and clinical management of HIV/AIDS.
Improving the Diagnosis and Management of Neuroendocrine Tumors: Utilizing New Advances in Biomarker and Molecular Imaging Science (2013)

Neuroendocrine tumors (NET) are malignant solid tumors that arise in hormone-secreting tissue of the diffuse neuroendocrine system or endocrine glands. Although traditionally understood to be a rare disease, the incidence and prevalence of NET have increased greatly in the past 3 decades. However, during this time, progress in diagnosis and outcome of NET has generally been modest. In order to achieve improved outcome in NET, a better understanding of NET biology combined with more reliable serum markers and better techniques to identify tumor localization and small lesions are needed. Although some NET biomarkers exist, sensitive and specific markers that predict tumor growth and behavior are generally lacking. In addition, the integration of new molecular imaging technologies in patient diagnosis and follow-up has the potential to enhance care. To discuss developments and issues required to improve diagnostics and management of NET patients, with specific focus on the latest advances in molecular imaging and biomarker science, 17 global leaders in the fields of NET, molecular imaging and biomarker technology gathered to participate in a 2-day meeting hosted by Prof. Kjell Öberg at the University of Uppsala in Sweden. During this time, findings were presented regarding methods with potential prognostic and treatment applications in NET or other types of cancers. This paper describes the symposium presentations and resulting discussions.
Biomedical research applications of a novel double‐layer parallel‐plate flow chamber (2007)

Shear stress‐mediated signaling pathways have been known to trigger endothelial cell responses and contribute to the pathophysiology of human vascular diseases. To study the dynamic response of endothelial cells to controlled levels of shear stress, we have recently developed a new double‐layer parallel‐plate flow chamber (PPFC). The present study was designed to test whether the novel PPFC can be applied to examine the effects of shear stress on the structure and function of endothelial cells. Rat brain endothelial cells (RBE4) and human microvascular endothelial cells (HMEC‐1) were either maintained in static condition or exposed to laminar flow for 24 h. The morphological changes and attenuated expression of pro‐inflammatory mediators were observed in endothelial cells exposed to the flow. In addition, RBE4 and HMEC‐1 cells were either maintained in continuous laminar flow condition ( Normal flow ) or subjected to 1 h of flow cessation followed by reperfusion of flow ( Ischemia/Reperfusion ). The real‐time RT‐PCR analysis showed that Ischemia/Reperfusion significantly up‐regulated expression of pro‐inflammatory mediators, such as IL‐6, ICAM‐1, VCAM‐1, and E‐selectin, in endothelial cells compared to Normal flow . These data indicate that our newly designed PPFC can provide a better in vitro system for versatile applications of biomedical research (This work was supported by the SBES Seed Grants).
Driver performance evaluation of two rear parking aids (2003)

Four levels of parking aids were tested using 32 participants in two age groups with equal numbers of men and women. Levels of parking aid were: no aid, ultrasonic rear park assist (URPA) with an auditory/visual distance to an object interface, a video view to the rear, and a combination of URPA with video view. Using a sport-utility vehicle, eighteen participants between 45 years and 55 years, and 14 participants 60 years and older performed five parking tasks: entering and exiting a parallel space, entering and exiting a perpendicular space, and backing to a trailer hitch. Participants reported higher scores of parking quality and judging distance to other objects with the video system than without. Objective measures including time to park, final position and angle in parking space showed differences based on parking aid system (URPA versus video). Age groups and replication number also showed differences. Total eye glance times to different areas of the vehicle showed differences based on parking aid system. For the covering abstract see ITRD E825082.
Towards Model-Based Testing with Architecture Models (2007)

As tools are maturing rapidly model-based testing is gaining wider attention by industry as a potential replacement for suite-based testing approaches. To use model-based testing tools users however specify often quite detailed test models, at level of the implementation to be tested. We present here a first attempt to generate tests from more abstract implementation models, which we call architecture models. With only little refinement these models can be used to validate implementations up to interaction accuracy. Our technique is applied to validate that the camera application software for Nokia Series 60 mobile devices conforms to its UML2 architecture model, employing the model-based testing tool Conformiq Qtronic
Palladium-Catalyzed Arylation and Acylation of 1-Benzyloxy-1,2,3-triazole Through a Directed Ortho Lithiation-Transmetalation Strategy (1998)

ortho-directed metalation - acylation - Pd(0)-catalysis - 1-benzyloxy-1,2,3-triazole - transmetalation
103Rh Chemical Shifts in Complexes Bearing Chelating Bidentate Phosphine Ligands (1999)

Experimental and theoretical methods have been employed to investigate the influence of the chelating phosphine ligand on the 103Rh chemical shift in complexes containing the [(P2)Rh] fragment (P2 = chelating bidentate phosphine). The δ(103Rh) values obtained by 2D(31P,103Rh{1H}) NMR spectroscopy for a series of neutral rhodium complexes [{R2P(CH2)nPR2}Rh(hfacac)] (R = Ar, Ph, Cy, Me, n = 1−4, hfacac = hexafluoroacetylacetonate) have been compared. Systematic variation of the phosphine ligand has allowed separation of electronic and geometrical effects. The purely electronic influence of para substituents in complexes [{(p-XC6H4)2P(CH2)4P(p-XC6H4)2}Rh(hfacac)] correlates directly with the Hammett σP constants of X, but leads to variations in the chemical shift of less than 80 ppm between X = CF3 and X = OMe. In contrast, geometrical changes in complexes [(P2)Rh(hfacac)] lead to variations in the chemical shift over a range of approximately 800 ppm. The individual contributions of various structural parameters on the δ(103Rh) values have been assessed by density-functional-based calculations for suitable model compounds. The same approach has been extended to the rationalization of the trends in 103Rh chemical shifts of cationic complexes with four P donor ligands around a Rh(+I) center and selected anionic Rh(−I) complexes [(P2)2Rh]-. This analysis allows for the first time a direct corroboration of geometrical variations and their effect on 103Rh chemical shifts, demonstrating that correlations of reactivity with 103Rh chemical shifts can give valuable information on structure/reactivity relationships.
DICTIONARY OF THE ECONOMIC PRODUCTS OF INDIA pages 561 to 569 (2014)

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Mapping Auto-context Decision Forests to Deep ConvNets for Semantic Segmentation (2015)

We consider the task of pixel-wise semantic segmentation given a small set of labeled training images. Among two of the most popular techniques to address this task are Decision Forests (DF) and Neural Networks (NN). In this work, we explore the relationship between two special forms of these techniques: stacked DFs (namely Auto-context) and deep Convolutional Neural Networks (ConvNet). Our main contribution is to show that Auto-context can be mapped to a deep ConvNet with novel architecture, and thereby trained end-to-end. This mapping can be used as an initialization of a deep ConvNet, enabling training even in the face of very limited amounts of training data. We also demonstrate an approximate mapping back from the refined ConvNet to a second stacked DF, with improved performance over the original. We experimentally verify that these mappings outperform stacked DFs for two different applications in computer vision and biology: Kinect-based body part labeling from depth images, and somite segmentation in microscopy images of developing zebrafish. Finally, we revisit the core mapping from a Decision Tree (DT) to a NN, and show that it is also possible to map a fuzzy DT, with sigmoidal split decisions, to a NN. This addresses multiple limitations of the previous mapping, and yields new insights into the popular Rectified Linear Unit (ReLU), and more recently proposed concatenated ReLU (CReLU), activation functions.
An Atlas of Variant Effects to understand the genome at nucleotide resolution (2023)

Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants, limiting opportunities for precision medicine and comprehension of genome function. A solution lies in experimental assessment of the functional effect of variants, which can reveal their biological and clinical impact. However, variant effect assays have generally been undertaken reactively for individual variants only after and, in most cases long after, their first observation. Now, multiplexed assays of variant effect can characterise massive numbers of variants simultaneously, yielding variant effect maps that reveal the function of every possible single nucleotide change in a gene or regulatory element. Generating maps for every protein encoding gene and regulatory element in the human genome would create an 'Atlas' of variant effect maps and transform our understanding of genetics and usher in a new era of nucleotide-resolution functional knowledge of the genome. An Atlas would reveal the fundamental biology of the human genome, inform human evolution, empower the development and use of therapeutics and maximize the utility of genomics for diagnosing and treating disease. The Atlas of Variant Effects Alliance is an international collaborative group comprising hundreds of researchers, technologists and clinicians dedicated to realising an Atlas of Variant Effects to help deliver on the promise of genomics.
Evaluation of Short Synthetic Antimicrobial Peptides against Staphylococcus pseudintermedius (2021)

Staphylococcus pseudintermedius infections present a serious challenge because of the emergence of resistance to numerous conventional antibiotics. Antimicrobial peptides are novel alternatives to traditional antibiotics due to their unique mechanism of action. In this study, we investigated the antibacterial activity of 12 short synthetic peptides against two clinical isolates of S. pseudintermedius isolated from two dog cases with ophthalmic lesions. In addition, the ability of the peptides to disrupt the established biofilm of these two S. pseudintermedius isolates was investigated. RRIKA and 5RHH showed good antimicrobial activity with MICs 2 and 4 µg/ml, respectively. IK8aIID and Indolicidin showed antimicrobial activity with MICs 8 and 16 µg/ml, respectively. Indolicidin, 5RHH and IK8aIID showed a significant biofilm mass % reduction up to 90%. Taken together, these results support the potential use of antimicrobial peptides for the treatment of S. pseudintermedius infections.
Robotic knot tying in minimally invasive surgeries (2003)

There have been many innovations introduced in securing tissues, but suturing with secure knots remains the most popular and cost effective method. However, knot tying demands higher level of skill on the surgeon, especially in the minimally invasive context. This paper presents the analytical and experimental results of automatic knot tying using an inhouse surgical robot with emphasis on the placement of the knot and tension regulation. The problem is decomposed to two parts: knot placement and knot tension control. The knot sliding condition is first obtained based on a simplified model of half knotted suture, and motion trajectories for the robots are proposed to minimize tearing trauma of the tissue while properly place the knot. The second half the paper considers the automatic tension regulation in the knot, which is usually difficult for the surgeon to achieve accurately. By using a cost effective means for tension measurement and applying the explicit force control algorithm with active damping, we are able to achieve stable and robust tension regulation. Experimental results are presented to demonstrate efficacy of the proposed algorithm.
Polygonization of binary classification maps using mesh approximation with right angle regularity (2018)

International audience
Cell-based siRNA screens highlight triple-negative breast cancer cell epigenetic vulnerability (2021)

&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt; Triple-negative breast cancer (TNBC) is a heterogeneous disease defined by ER-, PR- and HER2-negative phenotype and in most cases, a relatively aggressive clinical behaviour. The lack of specific targeted therapies and low efficiency of currently available chemotherapies spurred several clinical trials in the last few years. Despite encouraging results, TNBC still remains a major unmet medical need that prompted us to explore the role of 863 epigenetic modulators in TNBC cell survival.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods:&lt;/strong&gt; A comprehensive siRNA library was screened to explore the role of known epigenetic modulators in TNBC cell viability and growth. The knock-down effect was evaluated for 863 epigenetic genes using 4 siRNAs/gene in two TNBC and a non-TNBC cell lines using ATP-based luminescence and nuclei count image-based assays. Considering siRNA off-target effects, four analysis methods including a classical threshold-based analysis and three ranking methods were applied to determine on-target hits for each screen readout. Hit genes common to both phenotypic readouts highlighted strong epigenetic players involved in TNBC cell survival.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results:&lt;/strong&gt; Overall, knock-down of many epigenetic modulator genes mitigates cell survival in TNBC and a non-TNBC cell lines depicted from both phenotypic readouts. Interestingly, ranking-based analysis confirmed hit genes identified in threshold-based analysis and also revealed additional hits enabling us to confirm CDK1 and KMT5A as important regulators in TNBC cell viability and growth. Surprisingly, CHAF1A appeared as a new candidate gene involved in TNBC cell survival.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions:&lt;/strong&gt; Taken together, siRNA epigenetic screening results identified CHAF1A as a novel regulator of TNBC cell survival.&lt;/p&gt;
Physical Interaction Between Retinoic Acid Receptor and Sp1: Mechanism for Induction of Urokinase by Retinoic Acid (1999)

Induction of urokinase plasminogen activator (uPA) by retinoic acid (RA) is the initial event preceding certain subsequent biological changes in vascular endothelial cells. We investigated the molecular mechanism by which RA stimulates the expression of uPA, which lacks a canonical RA receptor (RAR)-responsive element, in bovine and human aortic endothelial cells. Upon stimulation with RA, mRNA levels of RARalpha and beta transiently increased in parallel with the induction of uPA, and this increase was inhibited by cycloheximide. Results of transient transfection of RAR/RXR cDNAs and experiments using specific agonists and antagonists suggested that uPA induction is dependent upon RAR (initially, RARalpha) with the help of RXRalpha. Deletion analysis of the uPA promoter suggested that RAR/RXR acts on GC box region within the uPA promoter. This was further supported by inhibition of Sp1 binding to this region. Coimmunoprecipitation studies, glutathione S-transferase pull-down experiment, and mammalian two-hybrid assays suggested a physical interaction between RAR/RXR and Sp1. Furthermore, gel shift studies showed that the binding of Sp1 to the uPA GC box is significantly potentiated in the presence of RARs/RXRs. Finally, Sp1 and RAR/RXR synergistically enhanced the transactivation activity of the uPA promoter. These results suggest that (1) RA induces RARs mainly via RARalpha and that (2) RAR/RXR physically and functionally interact with Sp1, resulting in a potentiation of uPA transcription.
Novel CR signal detection algorithms for coexistence in TV white space (2011)

In this paper, we propose novel signal detection algorithms for coexistence of CR systems in TV white space. As various CR standards appear in TV white space, technologies for detecting CR signals are required to enabling coexistence between CR systems. The proposed signal detection algorithms detect and classify CR networks utilizing cyclo-stationary features of each CR system. They consider multiple periodic properties of OFDM signal which is varied by parameters of each CR standard. The simulation results show that the proposed schemes can improve signal detection performance up to 50% compare with the conventional schemes.
Structural polymorphism of the luciferase gene in the firefly, Luciola lateralis (1999)

To study the structural features of genes for luciferase in Luciola lateralis, two different, functional luciferase genes, Luc1 and Luc2, were cloned and their nucleotide sequences were determined. The two genes were nearly identical, but a deletion of 128 bp was found in the 5' upstream region of Luc2, and minor deletions and additions were also found in the 3' downstream region. Seven base substitutions in the coding region produced two amino acid residue differences between the two genes. Southern blot analysis of genomic DNA isolated from 33 individual fireflies revealed that 26 were homozygous for the Luc1 gene and one was homozygous for Luc2. The others were heterozygotes with two, or even three, different alleles for the luciferase gene.