gebhart/patrepeval huggingface dataset:
An Overview on Single-Cell Technology for Hepatocellular Carcinoma Diagnosis (2022)

Hepatocellular carcinoma is a primary liver cancer caused by the accumulation of genetic mutation patterns associated with epidemiological conditions. This lethal malignancy exhibits tumor heterogeneity, which is considered as one of the main reasons for drug resistance development and failure of clinical trials. Recently, single-cell technology (SCT), a new advanced sequencing technique that analyzes every single cell in a tumor tissue specimen, aids complete insight into the genetic heterogeneity of cancer. This helps in identifying and assessing rare cell populations by analyzing the difference in gene expression pattern between individual cells of single biopsy tissue which normally cannot be identified from pooled cell gene expression pattern (traditional sequencing technique). Thus, SCT improves the clinical diagnosis, treatment, and prognosis of hepatocellular carcinoma as the limitations of other techniques impede this cancer research progression. Application of SCT at the genomic, transcriptomic, and epigenomic levels to promote individualized hepatocellular carcinoma diagnosis and therapy. The current review has been divided into ten sections. Herein we deliberated on the SCT, hepatocellular carcinoma diagnosis, tumor microenvironment analysis, single-cell genomic sequencing, single-cell transcriptomics, single-cell omics sequencing for biomarker development, identification of hepatocellular carcinoma origination and evolution, limitations, challenges, conclusions, and future perspectives.
Migration Inhibitory Activity in Serum and Cell Supernatants in Patients with Sezary Syndrome (1975)

The abnormal lymphocytes from patients with the Sezary syndrome produce macrophage migration inhibitory factors (MIF) both in vitro and in vivo. Five of six individuals studied had significant serum MIF activity and one had borderline activity. In contrast, in this study 47 normal individuals and 9 of 10 patients with extensive skin disease other than that of the Sezary syndrome had no such activity. Since the neoplastic T cells in patients with the Sezary syndrome localize in the skin, their production of chemical mediators in that site may be responsible for the generalized exfoliative erythroderma seen in that disease.
Identification of diphtheria toxin R domain mutants with enhanced inhibitory activity against HB-EGF (2014)

Heparin-binding epidermal growth factor-like growth factor (HB-EGF), a ligand of EGF receptor, is involved in the growth and malignant progression of cancers. Cross-reacting material 197, CRM197, a non-toxic mutant of diphtheria toxin (DT), specifically binds to the EGF-like domain of HB-EGF and inhibits its mitogenic activity, thus CRM197 is currently under evaluation in clinical trials for cancer therapy. To develop more potent DT mutants than CRM197, we screened various mutant proteins of R domain of DT, the binding site for HB-EGF. A variety of R-domain mutant proteins fused with maltose-binding protein were produced and their inhibitory activity was evaluated in vitro. We found four R domain mutants that showed much higher inhibitory activity against HB-EGF than wild-type (WT) R domain. These R domain mutants suppressed HB-EGF-dependent cell proliferation more effectively than WT R domain. Surface plasmon resonance revealed their higher affinity to HB-EGF than WT R domain. CRM197(R460H) carrying the newly identified mutation showed increased cell proliferation inhibitory activity and affinity to HB-EGF. These results suggest that CRM197(R460H) or other recombinant proteins carrying newly identified mutation(s) in the R domain are potential therapeutics targeting HB-EGF.
Supplementary Figure 3 from CD16<sup>+</sup>NKG2A<sup>high</sup> Natural Killer Cells Infiltrate Breast Cancer–Draining Lymph Nodes (2023)

&lt;p&gt;Supplementary Figure 3&lt;/p&gt;
THERMAL DECOMPOSITION OF THE LIGNIN MODEL COMPOUNDS: SALICYLALDEHYDE AND CATECHOL (2018)

The pure rotational spectrum of the AlC$_2$ radical (\\~{X}$^2$A$_1$) has been recorded for the first time using Fourier transform microwave/millimeter-wave (FTMmmW) techniques in the frequency range 21 – 65 GHz. AlC$_2$ was produced in a supersonic jet from the reaction of aluminum, generated by laser ablation, with a mixture of CH$_4$ or HCCH, diluted in argon, with a DC discharge. Three transitions ($N_{K_a,K_c}$ = 1$_{01}$ $\\rightarrow$ 0$_{00}$, 2$_{02}$ $\\rightarrow$ 1$_{01}$, and 3$_{03}$ $\\rightarrow$ 2$_{02}$) were measured, consisting of multiple fine/hyperfine components, resulting from the unpaired electron and the aluminum-27 nuclear spin ($I$ = 5/2). The data were analyzed using an asymmetric top Hamiltonian and rotational, fine structure, and hyperfine constants were established. These results are in excellent agreement with previous theoretical calculations and optical spectra. An $r_0$ structure of AlC$_2$ was determined to be $r$(Al–C) = 1.924 \\AA, $r$(C–C) = 1.260 \\AA, and $\\theta$(C–Al–C) = $38.2^{\\circ}$. The data are consistent with a T-shaped geometry with Al$^+$C$_2^-$ bonding. A search for AlC$_2$ in the circumstellar envelope of IRC+10216 is currently underway.
Evolutionary Engineering of a Cp*Rh(III) Complex-Linked Artificial Metalloenzyme with a Chimeric β-Barrel Protein Scaffold (2023)

Evolutionary engineering of our previously reported Cp*Rh(III)-linked artificial metalloenzyme was performed based on a DNA recombination strategy to improve its catalytic activity toward C(sp<sup>2</sup>)-H bond functionalization. Improved scaffold design was achieved with α-helical cap domains of fatty acid binding protein (FABP) embedded within the β-barrel structure of nitrobindin (NB) as a chimeric protein scaffold for the artificial metalloenzyme. After optimization of the amino acid sequence by directed evolution methodology, an engineered variant, designated NB<sup>HLH1</sup>(Y119A/G149P) with enhanced performance and enhanced stability was obtained. Additional rounds of metalloenzyme evolution provided a Cp*Rh(III)-linked NB<sup>HLH1</sup>(Y119A/G149P) variant with a >35-fold increase in catalytic efficiency (<i>k</i><sub>cat</sub>/<i>K</i><sub>M</sub>) for cycloaddition of oxime and alkyne. Kinetic studies and MD simulations revealed that aromatic amino acid residues in the confined active-site form a hydrophobic core which binds to aromatic substrates adjacent to the Cp*Rh(III) complex. The metalloenzyme engineering process based on this DNA recombination strategy will serve as a powerful method for extensive optimization of the active-sites of artificial metalloenzymes.
DC and Microwave Plasmas for Synthesis of Vertically Oriented Graphene (2014)

Plasma-enhanced chemical vapor deposition of vertically oriented graphene (VG) employing direct current glow discharge and microwave plasmas are presented and compared. The VG nanosheets with various morphologies can be obtained for diverse applications.
High-Density Single Nucleotide Polymorphism Array Defines Novel Stage and Location-Dependent Allelic Imbalances in Human Bladder Tumors (2005)

Bladder cancer is a common disease characterized by multiple recurrences and an invasive disease course in more than 10% of patients. It is of monoclonal or oligoclonal origin and genomic instability has been shown at certain loci. We used a 10,000 single nucleotide polymorphism (SNP) array with an average of 2,700 heterozygous SNPs to detect allelic imbalances (AI) in 37 microdissected bladder tumors from 17 patients. Eight tumors represented upstaging from Ta to T1, eight from T1 to T2+, and one from Ta to T2+. The AI was strongly stage-dependent as four chromosomal arms showed AI in > 50% of Ta samples, eight in T1, and twenty-two in T2+ samples. The tumors showed stage-dependent clonality as 61.3% of AIs were reconfirmed in later T1 tumors and 84.4% in muscle-invasive tumors. Novel unstable chromosomal areas were identified at chromosomes 6q, 10p, 16q, 20p, 20q, and 22q. The tumors separated into two distinct groups, highly stable tumors (all Ta tumors) and unstable tumors (2/3 muscle-invasive). All 11 unstable tumors had lost chromosome 17p areas and 90% chromosome 8 areas affecting Netrin-1/UNC5D/MAP2K4 genes as well as others. AI was present at the TP53 locus in 10 out of 11 unstable tumors, whereas 6 had homozygous TP53 mutations. Tumor distribution pattern reflected AI as seven out of eight patients with additional upper urinary tract tumors had genomic stable bladder tumors (P < 0.05). These data show the power of high-resolution SNP arrays for defining clinically relevant AIs.
Interconnected Fiber Network Prevents Gravel Washout in Water Injector Wells (2014)

Abstract In water injector wells, continuous injection can wash gravel from the annulus around the screen, especially if the rate of injection generates a pressure above the fracture threshold. The voids created after the washout are sometimes filled by an influx of formation sand during shut-in operations. This sand accumulation consequently reduces the injectivity when the injection operations resume. A solution to prevent such washouts is needed to maintain sand control and injectivity throughout the life of water injector wells. As a solution to this common problem, we propose a new fiber based product that reinforces the gravel and/or proppant pack. The fibers have an outside layer that is activated by temperature to form a bonded fiber network that locks the gravel in place. The fibers can be used with any type and size of proppant. The key benefit is that the fibers can withstand the cyclic loading of stress inherent to the shut-in and restart of injection operations, which are typically performed several hundred times during the life of an injector well. Our experimental study showed that the drag force of injected water easily displaced the gravel in the annulus into the fracture, whereas when gravel is reinforced with the fibers it withstood the drag force even at high injection rates (e.g., at 100 B/D per 0.5-in.-diameter perforation). We performed several experiments to evaluate the strength of the pack under cyclic stress conditions. After 30 cycles, the pack strength remained unaffected. The fiber chemistry was tailored for compatibility with commonly used fracturing fluids and brines. We found that the fibers remained connected in an interconnected network even after long-term interaction with seawater. We also studied the interaction of fibers with screens and other downhole equipment that comes in contact with the fibers during gravel placement. The laboratory results of that study showed the fibers do not create any issues with proppant placement or tool functionality during the sand control operation. Our experimental study also showed the fibers provided an effective solution for preventing gravel washout in water injector wells, thereby supporting the sand control and injectivity for the life of the well.
Atomic-resolution characterization of an SrTiO3 grain boundary in the STEM (1994)

High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted intuitively without the need for preconcieved atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementary chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25 degree symmetric tilt boundary in a bicrystal of the electroceramic SrTiO 3 . Figure 1(a) shows a Z-contrast image of a symmetric region of the tilt boundary. The brightest spots in the image correspond to the increased scattering power of the Sr atomic columns (Z=38) with theless bright spots corresponding to the Ti atomic columns (Z=22). The lighter O atomic columns are notvisible in a Z-contrast image.
Spectroscopy of the neutron-deficient isobars [sup 163]Re and [sup 163]W using tagging techniques (2008)

Selective tagging techniques have been used to establish new band structures in the transitional isobars 163Re and 163W. These nuclei were produced in the 106Cd(60Ni, xp yn γ) reaction at a bombarding energy of 270 MeV. Prompt γ rays were detected at the target position using the JUROGAM spectrometer while recoiling ions were separated by the RITU separator and implanted into the GREAT spectrometer. At low spin, the yrast band of 163Re is shown to be a strongly coupled collective band based on a proton h11/2 configuration. In 163W, the decay path of the 13/2+ isomeric state to the ground state has been identified and negative parity structures based on the ground state established.
Virtual optical interfaces for transportation (2009)

Today, the ever increasing number of controls in automobile and aviation cockpits leads to the cluttering of various interfaces (keyboards, switches, panels, etc...). LCD touch screens have proved to be a good alternative to reduce cluttering by reconfiguring in real time different interfaces, appearing on demand as they are needed by the user. However, the underlying screen still remains cumbersome and fragile glass device. We present a novel way to produce virtual consoles and interfaces by projecting diffractive images and sensing the position of the fingers by the use of IR diffractive optics.
ChromaBlur: Rendering Chromatic Eye Aberration Improves Accommodation and Realism in HMDs (2017)

We developed a rendering method that takes into account the eye’s chromatic aberration. Accommodation is driven much more accurately with this method than with conventional methods. Perceived realism is also improved.
Learning Fitness Functions for Genetic Algorithms (2019)

The problem of automatic software generation is known as Machine Programming. In this work, we propose a framework based on genetic algorithms to solve this problem. Although genetic algorithms have been used successfully for many problems, one criticism is that hand-crafting its fitness function, the test that aims to effectively guide its evolution, can be notably challenging. Our framework presents a novel approach to learn the fitness function using neural networks to predict values of ideal fitness functions. We also augment the evolutionary process with a minimally intrusive search heuristic. This heuristic improves the framework's ability to discover correct programs from ones that are approximately correct and does so with negligible computational overhead. We compare our approach with several state-of-the-art program synthesis methods and demonstrate that it finds more correct programs with fewer candidate program generations.
A MEMS-based Coupled-cavity Tunable Optical Filter (2006)

In this or we present the design of the first MEMS based tunable optical filter that satisfies a 20dB to 3dB bandwidth ratio of only 3. The design is based on the coupled cavity approach and its tuning is achieved using electrostatic actuation. The electro mechanical simulation using the finite element method (FEM) shows a settling time in the order of tens of microseconds.
A new low‐power driving method for high‐resolution mobile IPS LCDs (2010)

Abstract— High‐resolution displays are now needed for mobile equipment, not only for cell phones but for other devices such as ultra‐mobile PCs (UMPCs) and mobile Internet protocol televisions (IPTVs). A new low‐cost and low‐power driving method for high‐resolution in‐plane‐switching (IPS) liquid‐crystal displays (LCDs) on a low‐temperature polycrystalline‐silicon (LTPS) thin‐film‐transistor (TFT) platform has been developed. Because this method drives common electrodes separated by each line, it can reduce inversion frequency, unlike “dot‐inversion” or “column‐inversion” methods. On the other hand, it was found that horizontal smear is an obstacle to achieve this method. To solve this problem, techniques to optimize the timing of RGB time‐sharing are proposed. A 5‐in. WXGA (1366 × 768) prototype using the new driving method was fabricated, and it was found that the horizontal smear is less than ±1% of the luminance and that the power consumption of the display discharge and charge is 0.245 W.
Supplementary Figures from Clinical and Biological Subtypes of B-cell Lymphoma Revealed by Microenvironmental Signatures (2023)

&lt;p&gt;Supplementary Figures&lt;/p&gt;
Rapid Genome‐wide Single Nucleotide Polymorphism Discovery in Soybean and Rice via Deep Resequencing of Reduced Representation Libraries with the Illumina Genome Analyzer (2010)

Massively parallel sequencing platforms have allowed for the rapid discovery of single nucleotide polymorphisms (SNPs) among related genotypes within a species. We describe the creation of reduced representation libraries (RRLs) using an initial digestion of nuclear genomic DNA with a methylation‐sensitive restriction endonuclease followed by a secondary digestion with the 4bp‐restriction endonuclease DpnII . This strategy allows for the enrichment of hypomethylated genomic DNA, which has been shown to be rich in genic sequences, and the digestion with DpnII serves to increase the number of common loci resequenced between individuals. Deep resequencing of these RRLs performed with the Illumina Genome Analyzer led to the identification of 2618 SNPs in rice and 1682 SNPs in soybean for two representative genotypes in each of the species. A subset of these SNPs was validated via Sanger sequencing, exhibiting validation rates of 96.4 and 97.0%, in rice ( Oryza sativa ) and soybean ( Glycine max ), respectively. Comparative analysis of the read distribution relative to annotated genes in the reference genome assemblies indicated that the RRL strategy was primarily sampling within genic regions for both species. The massively parallel sequencing of methylation‐sensitive RRLs for genome‐wide SNP discovery can be applied across a wide range of plant species having sufficient reference genomic sequence.
In vivo validation and tissue sparing factor for acute damage of pencil beam scanning proton FLASH (2021)

The normal tissue sparing effect of PBS proton FLASH was validated. The FLASH factor was quantified through full dose response curves.
Self-Aligned Local Electrolyte Gating of 2D Materials for Mid-Infrared Photodetection (2017)

We present a new gating concept based on a self-aligned electrolyte technique that can enable spatially modulating charges with nanometer resolution. We use this technique to demonstrate a graphene mid-infrared thermopile photodetector with novel geometry.
Late embryogenesis abundant proteins protect human hepatoma cells during acute desiccation (2012)

Expression of late embryogenesis abundant (LEA) proteins is highly correlated with desiccation tolerance in anhydrobiotic animals, selected land plants, and bacteria. Genes encoding two LEA proteins, one localized to the cytoplasm/nucleus (AfrLEA2) and one targeted to mitochondria (AfrLEA3m), were stably transfected into human HepG2 cells. A trehalose transporter was used for intracellular loading of this disaccharide. Cells were rapidly and uniformly desiccated to low water content (<0.12 g H(2)O/g dry weight) with a recently developed spin-drying technique. Immediately on rehydration, control cells without LEA proteins or trehalose exhibited 0% membrane integrity, compared with 98% in cells loaded with trehalose and expressing AfrLEA2 or AfrLEA3m; surprisingly, AfrLEA3m without trehalose conferred 94% protection. Cell proliferation across 7 d showed an 18-fold increase for cells dried with AfrLEA3m and trehalose, compared with 27-fold for nondried controls. LEA proteins dramatically enhance desiccation tolerance in mammalian cells and offer the opportunity for engineering biostability in the dried state.
High-speed nano-imaging using dynamic mode AFM: A MAP detection approach (2010)

Nano-imaging has played a vital role in biology, chemistry and physics as it enables interrogation of material with sub-nanometer resolution. Primary means of achieving such atomic scale interrogation of matter are based on the principles of atomic force microscopy (AFM) and scanning tunneling microscopy (STM). However, current nano-imaging techniques are too slow to be useful in the high speed applications of interest such as studying the evolution of certain biological processes over time that involve very small time scales. In this work, we present a high speed one-bit imaging technique using dynamic mode AFM with a high quality factor cantilever. We model the high quality factor cantilever system using a Markovian model which incorporates the inherent system memory due to the inter-symbol interference and the cantilever state. Next, we pose the imaging problem as one of finding the maximum a posteriori (MAP) symbol detector for this model. This is solved by adapting the BCJR algorithm for our channel model. Furthermore, we propose an improved MAP symbol detector that incorporates a learned prior from the previous scan line while detecting the features on the current scan line. Experimental results demonstrate that our proposed algorithm provides significantly better image resolution compared to current nano-imaging techniques at high scanning speed.
Intraoperative implant rod three-dimensional geometry measured by dual camera system during scoliosis surgery (2016)

Treatment for severe scoliosis is usually attained when the scoliotic spine is deformed and fixed by implant rods. Investigation of the intraoperative changes of implant rod shape in three-dimensions is necessary to understand the biomechanics of scoliosis correction, establish consensus of the treatment, and achieve the optimal outcome. The objective of this study was to measure the intraoperative three-dimensional geometry and deformation of implant rod during scoliosis corrective surgery.A pair of images was obtained intraoperatively by the dual camera system before rotation and after rotation of rods during scoliosis surgery. The three-dimensional implant rod geometry before implantation was measured directly by the surgeon and after surgery using a CT scanner. The images of rods were reconstructed in three-dimensions using quintic polynomial functions. The implant rod deformation was evaluated using the angle between the two three-dimensional tangent vectors measured at the ends of the implant rod.The implant rods at the concave side were significantly deformed during surgery. The highest rod deformation was found after the rotation of rods. The implant curvature regained after the surgical treatment.Careful intraoperative rod maneuver is important to achieve a safe clinical outcome because the intraoperative forces could be higher than the postoperative forces. Continuous scoliosis correction was observed as indicated by the regain of the implant rod curvature after surgery.
Alpha interferon-induced antiretroviral activities: restriction of viral nucleic acid synthesis and progeny virion production in human immunodeficiency virus type 1-infected monocytes (1994)

Alpha interferon (IFN-alpha) restricts multiple steps of the human immunodeficiency virus type 1 (HIV-1) life cycle. A well-described effect of IFN-alpha is in the modulation of viral nucleic acid synthesis. We demonstrate that IFN-alpha influences HIV-1 DNA synthesis principally by reducing the production of late products of reverse transcription. The magnitude of IFN-alpha-induced downregulation of HIV-1 DNA and/or progeny virion production was dependent on the IFN-alpha concentration, the duration of cytokine administration, the multiplicity of infection, the viral strain, and the cycles of viral infection. Interestingly, reductions in viral DNAs could not fully account for the observed IFN-alpha-induced abrogation of progeny virion production. These data, by our investigation of both single-cycle and spreading viral infections, support a predominant but not exclusive effect of IFN-alpha on viral DNA synthesis.