gebhart/patrepeval huggingface dataset:
A method for systematically ranking therapeutic drug candidates using multiple uncertain screening criteria (2021)

Multiple different screening tests for candidate leads in drug development may often yield conflicting or ambiguous results, sometimes making the selection of leads a nontrivial maximum-likelihood ranking problem. Here, we employ methods from the field of multiple criteria decision making (MCDM) to the problem of screening candidate antibody therapeutics. We employ the SMAA-TOPSIS method to rank a large cohort of antibodies using up to eight weighted screening criteria, in order to find lead candidate therapeutics for Alzheimer's disease, and determine their robustness to both uncertainty in screening measurements, as well as uncertainty in the user-defined weights of importance attributed to each screening criterion. To choose lead candidates and measure the confidence in their ranking, we propose two new quantities, the Retention Probability and the Topness, as robust measures for ranking. This method may enable more systematic screening of candidate therapeutics when it becomes difficult intuitively to process multi-variate screening data that distinguishes candidates, so that additional candidates may be exposed as potential leads, increasing the likelihood of success in downstream clinical trials. The method properly identifies true positives and true negatives from synthetic data, its predictions correlate well with known clinically approved antibodies vs. those still in trials, and it allows for ranking analyses using antibody developability profiles in the literature. We provide a webserver where users can apply the method to their own data: http://bjork.phas.ubc.ca.
Investigating Guardian Awareness Techniques to Promote Safety in Virtual Reality (2023)

Virtual Reality (VR) can completely immerse users in a virtual world and provide little awareness of bystanders in the surrounding physical environment. Current technologies use predefined guardian area visualizations to set safety boundaries for VR interactions. However, bystanders cannot perceive these boundaries and may collide with VR users if they accidentally enter guardian areas. In this paper, we investigate four awareness techniques on mobile phones and smartwatches to help bystanders avoid invading guardian areas. These techniques include augmented reality boundary overlays and visual, auditory, and haptic alerts indicating bystanders' distance from guardians. Our findings suggest that the proposed techniques effectively keep participants clear of the safety boundaries. More specifically, using augmented reality overlays, participants could avoid guardians with less time, and haptic alerts caused less distraction.
Adaptive optical transmission for dynamic optical networks (2010)

Efforts towards commercializing higher-speed optical transmission have demonstrated the need for advanced modulation formats, several of which require similar transceiver hardware architecture. Adaptive transceivers can be built which have different operational configurations controlled by software. These software-defined transceiver configurations support a set of specific modulation / demodulation formats, with respective data rates and tolerances to system impairments, as well as sets of electronic digital signal processing schemes, chosen to best function in a given network environment. In this paper, we discuss possibilities and advantages of reconfigurable and dynamically-adaptive transceivers, and their potential applications in future optical networks.
ChemInform Abstract: Laser‐Enhanced Electrodeposition of Lead‐Tin Solder. (1992)

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.
A model-independent study of resonant structure in $B^+\to D^+D^-K^+$ decays (2020)

International audience
Prenatal Diagnosis of Placenta Accreta (2008)

Both sonography and MRI have fairly good sensitivity for prenatal diagnosis of placenta accreta; however, specificity does not appear to be as good as reported in other studies. In the case of inconclusive findings with one imaging modality, the other modality may be useful for clarifying the diagnosis.
Outcome of Latent Tuberculosis Infection in Solid Organ Transplant Recipients Over a 10-Year Period (2014)

A centralized referral program for LTBI therapy in transplant candidates is effective to prevent TB reactivation posttransplant. A significant proportion of liver transplant candidates and recipients do not tolerate standard LTBI therapy. Alternative therapies for these patients should be evaluated.
Obfuscation Mechanism in Conjunction with Tamper-Proof Module (2009)

This paper proposes a software obfuscation mechanism in conjunction with a tamper-proof module. The proposed mechanism overcomes the limitation of software-based obfuscation techniques where an obfuscated program contains critical parameters in itself. We divide a program into two parts: an obfuscated program and secret parameters. The obfuscated program is executed on a mobile phone or a computer, and it cannot be solely analyzed. An applet in the tamper-proof module securely stores the secret parameters and assists the execution of the obfuscation program. We implemented the proposed mechanism on a mobile phone and user identify module.The experiment results provide criteria for leveraging our obfuscation mechanism to protect both small-sized and large-sized programs.
Baseline Correction and Denoising of Raman Spectra by Deep Residual CNN (2020)

A practical deep residual CNN model for the improvement of Raman spectral analysis is proposed in this work. Through the feature transformation in the deep residual blocks, it successfully denoises and precisely corrects the baseline.
Radio-photoluminescence phenomenon in Ag-doped Cs2O–CaO–Al2O3–P2O5 glasses (2023)

Abstract In this study, Ag 2 O–Cs 2 O–CaO–Al 2 O 3 –P 2 O 5 glasses with different Ag concentrations (0, 0.1, 0.3, 1.0, and 3.0 mol.%) were made by the melt-quenching method. The photoluminescence (PL) properties, the radio-photoluminescence (RPL) phenomenon, and the spatial resolution of X-ray imaging based on RPL were studied to aim for the X-ray imaging application. The RPL phenomenon was observed as an appearance of a new PL emission at around 620 nm after X-ray irradiation. According to the shape of the PL spectrum and lifetime (13.1–16.7 ns), the luminescence was confirmed to be due to Ag 2+ . In addition, the 3.0% Ag-doped sample had the highest emission intensity of Ag 2+ . From the X-ray imaging resolution test, the 3.0% Ag-doped sample showed a spatial resolution of at least 10.0 LP mm −1 .
Unraveling the physicochemical and toxicological properties of food product isolated E341/E171 (2022)

Abstract Nanostructured materials have been extensively exploited in the food sector for nutrient delivery, sensing, packaging, and food additives. It has exhibited size, shape, chemical nature, and surface area‐dependent physicochemical and biological properties. Currently, nanoscale ingredients are identified in approved food additives. Still, food‐grade nanostructured material's impact on biological systems is unexplored well. Thus, in this study, we have identified and analyzed the physicochemical properties of nanoscale ingredients in commercial food product isolate E341 and E171 combinations. Also, we have evaluated the E341/E171 combination cytotoxic potential on human mesenchymal stem cells. The food isolated E341/E171 exhibits spherical nature with a 60–200 nm diameter. The E341 and E171 combination exposure increased the cell viability loss to ~36% at a high dose in human mesenchymal stem cells (hMSCs). The E341/E171 treatment‐induced cellular and nuclear damage at a moderate dose. The mitochondrial membrane potential loss and ROS generation were observed in E341/E171 treated cells. The E341/E171 alters the gene expression pattern in hMSCs dose‐dependently. The GSR and POR gene expression is upregulated significantly in E341/E171 treatment. Our study results revealed that E341/E171 induced toxicity in hMSCs at high concentrations. Thus, E341/E171 potential impact on the biological system should be reexamined for food industrial implications.
The world in an eye (2004)

This paper provides a comprehensive analysis of exactly what visual information about the world is embedded within a single image of an eye. It turns out that the cornea of an eye and a camera viewing the eye form a catadioptric imaging system. We refer to this as a corneal imaging system. Unlike a typical catadioptric system, a corneal one is flexible in that the reflector (cornea) is not rigidly attached to the camera. Using a geometric model of the cornea based on anatomical studies, its 3D location and orientation can be estimated from a single image of the eye. Once this is done, a wide-angle view of the environment of the person can be obtained from the image. In addition, we can compute the projection of the environment onto the retina with its center aligned with the gaze direction. This foveated retinal image reveals what the person is looking at. We present a detailed analysis of the characteristics of the corneal imaging system including field of view, resolution and locus of viewpoints. When both eyes of a person are captured in an image, we have a stereo corneal imaging system. We analyze the epipolar geometry of this stereo system and show how it can be used to compute 3D structure. The framework we present in this paper for interpreting eye images is passive and non-invasive. It has direct implications for several fields including visual recognition, human-machine interfaces, computer graphics and human affect studies.
Epidermal growth factor and basic fibroblast growth factor suppress the spontaneous onset of apoptosis in cultured rat ovarian granulosa cells and follicles by a tyrosine kinase-dependent mechanism. (1992)

Recent biochemical studies have suggested that apoptotic cell death is the molecular mechanism underlying the degeneration of ovarian follicles during atresia. Using a sensitive autoradiographic method for the detection of DNA fragmentation, we studied apoptosis in ovarian granulosa cells or intact follicles placed in serum-free culture as model systems to elucidate the hormonal regulation of atresia. Immature rats (25 days old) were primed for 2 days with 10 IU equine CG to induce a homogeneous population of mature preovulatory follicles. Granulosa cells isolated from these follicles contained predominantly intact high mol wt DNA. However, a time-dependent, spontaneous onset of internucleosomal DNA fragmentation characteristic of apoptotic cell death occurred in granulosa cells during culture. Treatment of granulosa cells with epidermal growth factor (EGF), transforming growth factor-alpha (TGF alpha), or basic fibroblast growth factor (bFGF) inhibited the spontaneous onset of apoptotic DNA cleavage found during culture by 40-60%. In contrast, insulin-like growth factor I, insulin, TGF beta and tumor necrosis factor-alpha were ineffective. Likewise, activation of the protein kinase A or C pathways with forskolin or phorbol 12-myristate 13-acetate, respectively, did not prevent the onset of DNA fragmentation, although inclusion of a tyrosine kinase inhibitor (genistein) completely blocked the ability of EGF, TGF alpha, and bFGF to suppress apoptosis in granulosa cells. Similar to cultured granulosa cells, a spontaneous onset of apoptosis was also observed to occur in isolated preovulatory follicles during culture. Furthermore, treatment of follicles with EGF or bFGF inhibited the spontaneous initiation of apoptosis, and the suppressive effects of these growth factors were also attenuated by co-treatment with genistein.(ABSTRACT TRUNCATED AT 250 WORDS)
Compact Modeling of SOI MOSFETs With Ultrathin Silicon and BOX Layers (2014)

The reported compact SOI-MOSFET model hiroshima university starc igfet model-silicon on thin buried oxide (HiSIM-SOTB) has been developed for devices with ultrathin silicon on insulator (SOI) and buried oxide (BOX) layers. The potential distribution determined by the Poisson equation is accurately solved with the Newton iteration method across the SOI layer and in the substrate on the backside of the BOX for source and drain side of the device. All charges including accumulation and inversion charges on both side of the BOX are explicitly considered in the Poisson equation. It is found that different from the double-gate MOSFET, the influence of the impurity concentration of the bulk substrate below the BOX must be also explicitly considered to capture all measured properties of the silicon on thin buried oxide (SOTB) MOSFET. A further modeling challenge of the thin SOI and BOX layers, which had to be overcome, is that charge neutrality is not independently preserved at the front-gate oxide or at BOX side, but only totally within the whole device. Additionally it is found that, due to the consistent potential- and charge-based model formulation, the developed HiSIM-SOTB model can reproduce not only TCAD and measured SOTB device data but is even capable to predict the effects of structural variations, including the limiting case of the double-gate MOSFET structure.
Intranasal inoculation of Cryptococcus neoformans in mice produces nasal infection with rapid brain dissemination (2019)

Abstract Cryptococcus neoformans is an important fungal pathogen, causing life-threatening pneumonia and meningoencephalitis. Brain dissemination of C. neoformans is thought to be a consequence of an active infection in the lung which then extravasates to other sites. Brain invasion results from dissemination via the bloodstream, either by free yeast cells in bloodstream or Trojan horse transport within mononuclear phagocytes. We assessed brain dissemination in three mouse models of infection: intravenous, intratracheal, and intranasal. All three modes of infection resulted in dissemination of C. neoformans to the brain in under 3 hours. Further, C. neoformans was detected in the entirety of the upper respiratory tract and the ear canals of mice. In recent years, intranasal infection has become a popular mechanism to induce pulmonary infection because it avoids surgery but our findings show that instillation of C. neoformans produces cryptococcal nasal infection. These findings imply that immunological studies using intranasal infection should assume the initial sites of infection of infection are brain, lung and upper respiratory tract, including the nasal airways. Importance Cryptococcus neoformans causes an estimated 181, 000 deaths each year, mostly associated with untreated HIV/AIDS. C. neoformans has a ubiquitous worldwide distribution. Humans become infected from exposure to environmental sources and the fungus lays dormant within the human body. Upon immunosuppression, such as AIDS or therapy-induced as required by organ transplant recipients or autoimmune disease patients, cryptococcal disease reactivates and causes life-threatening meningitis and pneumonia. This study has detected that upon contact with the host, C. neoformans can quickly (a few hours) reach the host brain and will also colonize the nose of infected animals. Therefore, this work paves the way to better knowledge of how C. neoformans travels through the host body. Understanding how C. neoformans infects, disseminates and survives within the host is critically required so that we can prevent infections and the disease caused by this deadly fungus.
Bi-SQUID arrays and parallel SQIF structures for active electrically small antennas (2012)

The basic physics of the development of broadband active electrically small superconductive antennas for the subgigahertz and gigahertz frequency ranges, based on series arrays with cells characterized by a highly linear voltage response to the magnetic component B of an electromagnetic signal, are under consideration. As such cells, bi-SQUIDs and cells based on two parallel SQIF structures that are differentially connected are proposed. Series arrays of cells with linear voltage response, including an antenna prototype, are fabricated using standard niobium technology with a critical current density of Josephson junctions of 4.5 kA/cm2 and are studied experimentally. The data obtained allow estimation of the achievable dV/dB conversion factor and the sensitivity δB for an antenna integrated with a magnetic flux converter, placed on an available area of 3.3 × 3.3 mm of a chip 5 × 5 mm in size. These values are found to be 10 μV/nT and 20 fT/Hz1/2, respectively. The conversion factor increases in proportion with the area a 2 occupied by the antenna with a square flux converter, and the sensitivity is improved as a −3/2.
Supplementary Figure 1 from p53–Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT (2023)

&lt;p&gt;The protein levels of Twist1 (A) and p53 (B) in tumor samples. Protein levels were determined by the quantification of western blot band intensity comparing to GAPDH bands as loading control.&lt;/p&gt;
Emissive Iridium(III) Diimine Complexes Formed by Double Cyclometalation of Coordinated Triphenylphosphite (2011)

We report on the synthesis of a new series of iridium(III) complexes functionalized with various diimine chromophores, together with a facially coordinated dicyclometalated phosphite chelate and a monodentate anionic ancillary. This conceptual design presents a novel strategy in obtaining a new class of iridium(III) diimine complexes without employment of traditional nitrogen-containing polyaromatic cyclometalates. Additionally, we discuss the basic charactersistics of the ground and lower-lying excited states involved, as documented by crystal structural, photophysical studies, and density functional theory calculations. Fabrication of the green-emitting organic light-emitting diodes with one such dopant, [Ir(dbbpy)(tpit)NCS] (2b), where dbbpy and tpit represent di-tert-butyl-2,2'-bipyridine and dicyclometalated triphenylphosphite, respectively, was successfully made, attaining a peak external quantum efficiency (η(ext)), a luminance efficiency (η(l)), and a power efficiency (η(p)) of 14.1%, 46.6 cd A(-1), and 39.9 lm W(-1), respectively.
PGP1 personal genome assembly - a hybrid assembly dataset using ONT’s PromethION and PacBio’s HiFi sequencing (2021)

Abstract PGP1 is the first participant of Personal Genome Project. We present the PGP1’s chromosome-scale genome assembly. It was constructed using 255 Gb ultra-long PromethION reads and 97 Gb short paired-end reads. For reducing base calling errors, we corrected PromethION reads using 72 Gb PacBio HiFi reads. 327 Gb Hi-C chromosomal mapping data were utilized to maximize the assembly’s contiguity. PGP1’s contig assembly was 3.01 Gb in length comprising of 4,234 contigs with an N50 value of 33.8 Mb. After scaffolding with Hi-C data and extensive manual curation, we obtained a chromosome-scale assembly that represents 3,880 scaffolds with an N50 value of 142 Mb. From the Merqury assessment, PGP1 assembly achieved a high QV score of Q45.45. For a gene annotation, we predicted 106,789 genes with a liftover from the Gencode 38 and an assembly of transcriptome data.
Tracking MSE performance analysis of the &#x2208;-NSLMS algorithm (2015)

In this paper, the tracking behavior of the ∈-normalized sign-error least mean square (NSLMS) algorithm is analyzed in the presence of white and correlated Gaussian regressors. Moreover, generic analytical expressions are derived for the optimal step-size and the corresponding optimal meansquare error (MSE) of the ∈-NSLMS algorithm for both the real- and complex-valued data cases. Additionally, a comparison between the convergence behavior of the ??-NSLMS algorithm and the ∈-normalized least mean square (NLMS) algorithm is also discussed. Finally, simulation results to corroborate our theoretical findings are presented.
Tissue‐Engineered Blood Vessels (2005)

This chapter contains sections titled: Background Preparation of Media and Reagents Culture of Tissue-Engineered Vascular Grafts Characterization of Engineered Vessels Discussion Acknowledgments Sources of Materials References
Purification and characterization of a membrane-associated 3,3',5-triiodo-L-thyronine binding protein from a human carcinoma cell line. (1986)

A membrane-associated binding protein for 3,3',5-triiodo-L-thyronine (T3) was purified to apparent homogeneity from A431 human epidermoid carcinoma cells. A431 cells were specifically labeled with the N-bromoacetyl derivative of T3 labeled with 125I at the 3' position (BrAc[125I]T3) and were extracted with 3-[3-(cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), a zwitterionic detergent. The solubilized BrAc[125I]T3-labeled protein was successively purified by chromatography on Sephadex G-200 and QAE-Sephadex followed by NaDod-SO4/PAGE. Approximately 0.2 mg of purified protein was obtained from 2.5 X 10(9) cells, which represents a 3000-fold purification. The membrane-associated T3 binding protein is an acidic protein with a pI of 5.1 and an apparent molecular mass of 55,000 daltons determined by NaDodSO4/PAGE. Polyclonal antibodies against the 55-kDa protein were prepared and used in indirect immunofluorescence to show that the 55-kDa protein was mainly found in the nuclear envelope and endoplasmic reticulum.
The Cotton Centromere Contains a Ty3-gypsy-like LTR Retroelement (2012)

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species.