gebhart/patrepeval huggingface dataset:
The lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity (2021)

ABSTRACT Objective The study objective was to compare gut microbiome diversity and composition in SARS-CoV-2 polymerase chain reaction (PCR)-positive patients whose symptoms ranged from asymptomatic to severe, versus PCR-negative exposed controls. Design Using a cross-sectional design, we performed shotgun next-generation sequencing (NGS) on stool samples to evaluate gut microbiome composition and diversity in both patients with SARS-CoV-2 PCR- confirmed infections, that had presented to Ventura Clinical Trials for care from March 2020 through October 2021, and SARS-CoV-2 PCR-negative exposed controls. Patients were classified as being asymptomatic or having mild, moderate, or severe symptoms based on NIH criteria. Exposed controls were individuals with prolonged or repeated close contact with patients with SARS-CoV-2 infection or their samples, e.g. household members of patients or frontline healthcare workers. Microbiome diversity and composition were compared between patients and exposed controls at all taxonomic levels. Results Compared with controls (n=20), severely symptomatic SARS-CoV-2 infected patients (n=28) had significantly less bacterial diversity (Shannon Index, P=0.0499; Simpson Index, P=0.0581), and positive patients overall had lower relative abundances of Bifidobacterium (P&lt;0.0001), Faecalibacterium (P=0.0077), and Roseburium (P=0.0327), while having increased Bacteroides (P=0.0075). Interestingly, there was an inverse association between disease severity and abundance of the same bacteria. Conclusion We hypothesize that low bacterial diversity and depletion of Bifidobacterium genera either before or after infection led to reduced pro-immune function, thereby allowing SARS-CoV-2 infection to become symptomatic. This particular dysbiosis pattern may be a susceptibility marker for symptomatic severity from SARS-CoV-2 infection and may be amenable to pre-, intra-, or post infection intervention. Keywords: SARS-CoV-2, COVID, Microbiome, Bifidobacterium, Faecalibacterium, Bacteriodes, Shannon Index, Simpson Index, Severity, Microbiota Registration clinicaltrials.gov NCT04031469 (PCR -) and 04359836 (PCR+)
Dendritic cell derived-exosomes: biology and clinical implementations (2006)

Exosomes are nanometer-sized membrane vesicles invaginating from multivesicular bodies and secreted from different cell types. They represent an "in vitro" discovery, but vesicles with the hallmarks of exosomes are present in vivo in germinal centers and biological fluids. Their protein and lipid composition is unique and could account for their expanding functions such as eradication of obsolete proteins, antigen presentation, or "Trojan horses" for viruses or prions. The potential of dendritic cell-derived exosomes (Dex) as cell-free cancer vaccines is addressed in this review. Lessons learned from the pioneering clinical trials allowed reassessment of the priming capacities of Dex in preclinical models, optimizing clinical protocols, and delineating novel, biological features of Dex in cancer patients.
Bone Marrow Versus Peripheral Blood Progenitor Cells CD34 Selection in Patients With Non-Hodgkin's Lymphomas: Different Levels of Tumor Cell Reduction. Implications for Autografting (1997)

Human CD34+ selected cells are able to reconstitute hematopoiesis in patients receiving a myeloablative treatment. Although the role of reinfused tumor cells contaminating the grafts on the determination of postautograft relapses remains unclear, the major interest of CD34+ cell selection is to reduce the tumor contamination of the graft. This can be achieved if tumor cells do not express the CD34 antigen. We previously showed that this approach was effective with bone marrow (BM) collections in patients with non-Hodgkin's lymphoma (NHL). Because peripheral blood progenitor cells (PBPC) allow faster hematologic recovery than BM and are expected to contain less tumor contamination, we have compared the results of CD34+ cell selection in 35 BM and 16 PBPC from 48 patients with NHL. The PBPC were collected after a course of chemotherapy followed by granulocyte colony-stimulating factor (G-CSF ) administration. The data showed that the final CD34+ cell purity achieved with PBPC was higher than with BM (medians, 70% v 50%; P = .02). The CD34+ cell recovery was also better for PBPC (medians, 42% v 24%; P = .001). Tumor contamination was assessed by detection of BCL2/JH rearrangement using polymerase chain reaction (PCR) in 38 of 48 patients (22 BM, 16 PBPC). In addition, immunoglobulin heavy chain gene (IgH) rearrangements were investigated using PCR with consensus IgH primers. At harvesting, 10 of 22 BM and two of 16 PBPC contained BCL2/JH+ cells, one of 22 BM and 14 of 16 PBPC contained abnormal IgH+ cells (one PBPC contained both BCL2/JH+ and abnormal IgH+ cells) at harvesting. However, because lymphoma tissue specimens from patients at diagnosis were not available, the malignant character of IgH rearrangements could not be confirmed by sequencing and probing with allele-specific nucleotides. After CD34+ cell selection, a reduction to below the level of detection of BCL2/JH+ cells of BM and PBPC was effective in seven of 12 informative selections. In contrast, a reduction to below the level of detection of abnormal IgH+ cells was effective in only three of 15 informative selections. However, the detection of cells with an abnormal IgH pattern in the context of chemotherapy plus G-CSF progenitor mobilization in patients with NHL and its correlation with actual tumor contamination needs further investigation.
Abstract 320: Heterogeneous Coronary Stent Inflammation and Healing Revealed by in vivo Optical Molecular-Structural Imaging (2013)

Introduction Patients with diabetes mellitus that receive coronary stents experience greater stent restenosis and thrombosis, leading to adverse clinical outcomes. Impaired stent healing is linked to elevated endovascular inflammation, but in vivo data is lacking. Here, we assessed stent inflammation and tissue healing in diabetic rabbits, using intravascular molecular-structural near-infrared fluorescence (NIRF)-optical frequency domain imaging (OFDI). Methods A bare-metal stent (3.5x12mm) was implanted in the infrarenal aorta of alloxan-induced diabetic rabbits (n=5). At day 28, intravascular NIRF-OFDI was performed. Prosense VM110 (5mg/kg IV 24 hrs before imaging; ex/em 750/780 nm) enabled NIRF molecular imaging of inflammatory cathepsin activity. Structural OFDI stent endothelialization (coverage) was simultaneously assessed in 0.5mm intervals. Aortas were then harvested for ex vivo fluorescence reflectance imaging (FRI), electrochemical stent dissolution, and cathepsin B immunostaining. Results At day 28, stent NIRF inflammatory cathepsin protease activity was enhanced compared to the non-stented aorta (50.9±2.0 vs. 26.1±0.6 nM; p&lt;0.0001). OFDI demonstrated greater average stent edge restenosis (proximal and distal 2mm stent edge neointimal area, 1.63±0.12 vs. mid 2 mm stent 0.50±0.05 mm 2 ; p&lt;0.0001), with less de-endothelialized struts at the stent edges (2.1±1.7% vs. 14.0±4.1% mid stent; p=0.03). Stent edge NIRF inflammation was also greater (60.8±3.4 vs. 40.8±1.4 nM mid stent; p=0.0005), and correlated with neointima formation (R=0.43; p=0.003). Conversely, NIRF inflammation negatively tracked with OFDI-uncovered stent struts (R=-0.42; p=0.004). FRI corroborated the enhanced stent-edge NIRF pattern. Matched histopathology revealed cathepsin B expression in NIRF-positive regions. Conclusions Intravascular NIRF-OFDI molecular-structural imaging demonstrates that NIRF inflammatory protease activity is linked to increased bare-metal stent edge neointimal formation, but inversely relates to uncovered stent struts. This translatable approach provides new insights into stent inflammation and healing, and may ultimately inform the risk of stent restenosis and thrombosis.
Ultra-High Data-Rate 60 GHz Radio-over-Fiber Systems Employing Optical Frequency Multiplication and Adaptive OFDM Formats (2011)

This paper reviews 60-GHz radio-over-fiber systems employing optical frequency multiplication and adaptive OFDM signals with multi-level modulation formats to achieve an ultra-high data rate of up to 32.65 Gbps within the 7-GHz license-free band.
Detection of colorectal neoplasia associated K-Ras mutations in human urine (2006)

1005 Background: Since colorectal neoplasia-associated genes have been detected in human blood, we hypothesized that small DNA fragments containing genetic mutations associated with colorectal neoplasias are filtered and excreted in the urine. If so, genes associated with colorectal cancer will be detected in the urine. K-ras mutations are commonly associated with colorectal neoplasia and do not occur in the urinary tract. Methods: K-ras mutation detection: 200 microl of urine was extracted with guanidine thiocyanate and purifed using a Wizard DNA isolation kit. Codon 12 K-ras mutation detection methods–1: restriction enriched PCR, 20 cycles, with primers that amplify both wild type and mutated DNA but with an artificial BstNI site at the 5’ end of the amplified product (&gt;2 K-ras copies per assay); 2: Peptide nucleic acid clamping real time PCR (&gt;15 K-ras copies per assay). Human subjects: Training set = 20 patients with known K-ras mutations in colorectal cancer tissue. Test set = blinded urine samples from colorectal adenocarcinoma (N=48), adenoma (N=31), hyperplastic polyp (N=12) and endoscopically normal colon and rectum (N=60). Results: 1. Human urine contains 150–250 base pair DNA fragments derived from the circulation. These fragments can be readily distinguished from high molecular weight DNA from sloughed urinary tract cells. 2. Training set for K-ras detection (tissue confirmed K-ras mutations): Serum 6/20 (30%), Plasma (11/20 (55%), Urine: 18/20 (90%), (p&lt;0.15 for plasma, p&lt;0.001 for serum). 3. Test set (blinded): a. &gt;2 copies of mutated K-ras genes were detected in: 16/48 (33%) adenocarcinomas; 23/31 (74%) adenomas; 5/12 (42%) hyperplastic polyps, and 19/60 (31%) non-neoplasia controls. b. &gt;15 copies of mutated K-ras genes were detected in: 12/48 (25%) adenocarinomas; 15/31 (48%) adenomas; 3/12 (25%) hyperplastic polyps, and 11/60 (18%) non-neoplasia controls. Conclusions: Small DNA fragments in human urine contain K-Ras mutations identical to those found in colorectal cancer DNA. The sensitivity for detection of K-ras mutations in urine appears equivalent or superior to K-ras mutation detection in feces or serum. DNA mutations from systemic epithelial neoplasias may be detected in filtered urinary DNA fragments and may be useful for early detection of neoplasia. No significant financial relationships to disclose.
Hardware Solutions for 5G Mobility (2018)

For 5G mobility, the form factors that are familiar with today may be kept the same (such as those in smartphones and iPads) or to be replaced by even smaller ones, such as, a watch, or wearables. In this chapter, the authors present the IC packaging technologies that are on the horizon. They expand the hardware scope to include these components: the multi-mode multi-band (MMMB) modem, and the WPAN radio. The authors introduce planar technologies such as, wafer-level planar (WLP) and large panel planar (LPP) and advanced interconnects for 2.5D and 3D stacking for 5G products. They discuss packaging forms and planar solutions to high-density and logic (HD&L) and RF-passives products. The authors also discuss future business model. STATS proposed the following model, post wafer fab processing (PWfP) that is significantly from the current wafer foundries (WFs) and OSAT business model.
Expression of X-Linked Inhibitor of Apoptosis Protein (XIAP) in Breast Cancer Is Associated with Shorter Survival and Resistance to Chemotherapy (2021)

XIAP, the most potent inhibitor of cell death pathways, is linked to chemotherapy resistance and tumor aggressiveness. Currently, multiple XIAP-targeting agents are in clinical trials. However, the characterization of XIAP expression in relation to clinicopathological variables in large clinical series of breast cancer is lacking. We retrospectively analyzed non-metastatic, non-inflammatory, primary, invasive breast cancer samples for <i>XIAP</i> mRNA (<i>n</i> = 2341) and protein (<i>n</i> = 367) expression. XIAP expression was analyzed as a continuous value and correlated with clinicopathological variables. <i>XIAP</i> mRNA expression was heterogeneous across samples and significantly associated with younger patients' age (≤50 years), pathological ductal type, lower tumor grade, node-positive status, HR+/HER2- status, and PAM50 luminal B subtype. Higher XIAP expression was associated with shorter DFS in uni- and multivariate analyses in 909 informative patients. Very similar correlations were observed at the protein level. This prognostic impact was significant in the HR+/HER2- but not in the TN subtype. Finally, <i>XIAP</i> mRNA expression was associated with lower pCR rate to anthracycline-based neoadjuvant chemotherapy in both uni- and multivariate analyses in 1203 informative patients. Higher XIAP expression in invasive breast cancer is independently associated with poorer prognosis and resistance to chemotherapy, suggesting the potential therapeutic benefit of targeting XIAP.
A real time optical strain sensor based on a cholesteric liquid crystal network (2013)

A flexible, strain sensor for monitoring uniaxial deformations in oriented polymer films is demonstrated. The sensor consists of a crosslinked cholesteric liquid crystal layer which is spray-coated on a uniaxially oriented polyamide 6 substrate. When no deformation is applied, reflectivity measurements showed a well-defined reflection band. Upon uniaxial extension, the reflection band shifted towards lower wavelengths. A 40 nm shift was recorded for 13% of strain. This wavelength shift is attributed to a decrease in the cholesteric helix's pitch which is induced by the change in thickness of the CLC coating due to Poisson's contraction. As a result the colour of the film changed from orange to green with increasing strain. The optical response was found to follow the mechanical behaviour of the polymer substrate. Cycling loading showed a time dependent optical response of the sensor fitting with the viscoplastic mechanical response of the substrate giving real time information on the deformation.
The Ultimate in Cancer Chemoprevention: Cancer Vaccines (2010)

This perspective on Beatty et al. (beginning on page 438 in this issue of the journal) discusses the role of the immune system as nature's ultimate chemoprevention agent. A successful immune response to vaccination results in immunologic memory. In the case of a successful cancer-related response, antigen-specific T cells will be poised to destroy an aberrantly expressed protein even if the host is not exposed until years after the end of immunizations. After the abnormal cell is eradicated, T cells will lie in wait for the next exposure. The ability to develop effective cancer vaccines for prevention is fast becoming a reality as immunogenic aberrant proteins that drive malignant transformation are identified.
Structure of the (E)‐4‐hydroxy‐3‐methyl‐but‐2‐enyl‐diphosphate reductase from Plasmodium falciparum (2013)

Terpenoid precursor biosynthesis occurs in human and many pathogenic organisms via the mevalonate and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, respectively. We determined the X-ray structure of the Fe/S containing (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase (LytB) of the pathogenic protozoa Plasmodium falciparum which catalyzes the terminal step of the MEP pathway. The cloverleaf fold and the active site of P. falciparum LytB corresponds to those of the Aquifex aeolicus and Escherichia coli enzymes. Its distinct electron donor [2Fe-2S] ferredoxin was modeled to its binding site by docking calculations. The presented structural data provide a platform for a rational search of anti-malarian drugs.
Supplementary Tables S1-S2 from Potent siRNA Inhibitors of Ribonucleotide Reductase Subunit RRM2 Reduce Cell Proliferation <i>In vitro</i> and <i>In vivo</i> (2023)

Supplementary Tables S1-S2 from Potent siRNA Inhibitors of Ribonucleotide Reductase Subunit RRM2 Reduce Cell Proliferation &lt;i&gt;In vitro&lt;/i&gt; and &lt;i&gt;In vivo&lt;/i&gt;
Correlation histogram analysis of depth-enhanced 3D video coding (2010)

This paper introduces a correlation histogram method for analyzing the different components of depth-enhanced 3D video representations. Depth-enhanced 3D representations such as multi-view video plus depth consist of two components: video and depth map sequences. As depth maps represent the scene geometry, their characteristics differ from the video data. We present a comparative analysis that identifies the significant characteristics of the two components via correlation histograms. These characteristics are of special importance for compression. Modern video codecs like H.264/AVC are highly optimized to the statistical properties of natural video. Therefore the effect of compressing the two components using the MVC extension of H.264/AVC is evaluated in the second part of the analysis. The presented results show that correlation histograms are a powerful and well-suited method for analyzing the impact of processing on the characteristics of depth-enhanced 3D video.
Determination of the Rate Constant for Soot Surface Growth (1983)

Abstract The total mass of soot in a premixed flat flame increases steeply with time through a process known as surface growth. In this paper we show that the surface growth rate is first order in the acetylene concentration, and we measure the apparent first order rate constant. We also show that the surface growth rate is not strongly temperature dependent, It is suggested that the C/H ratio of the soot may be important in determining its reactivity.
SPECTROSCOPIC EVIDENCE FOR LOW TEMPERATURE STRUCTURAL CHANGES IN BIPHENYL CRYSTALS (1973)

Temperature dependent studies of the Raman, infrared and far infrared spectra of both neat and isotopically mixed biphenyl crystals reveal significant changes in the spectra as the temperature is lowered below $50^{\\circ} K$. These changes suggest that the biphenyl crystal undergoes a structural change at low temperature. Further evidence is provided by the study of the $2^{\\circ} K$ fluorescence and phosphorescence spectra of the dilute isotopic mixed biphenyl crystal, where we have observed site splittings. These site splittings have also been reported recently by Hochstrasser et $al.^{1}$ The nature of the structural change will be discussed.
Patient-specific computational fluid dynamics analysis of transcatheter aortic root replacement with chimney coronary grafts (2020)

The proposed numerical simulations, in the specific case under investigation, suggest that the TARR technique maintains coronary perfusion through the chimney grafts. This study calls for experimental validation and further analyses of the impact of TARR on cardiac afterload, decrease of aortic compliance and local pressure drop induced by the coronary chimney grafts.
Western blot detection of IgG anti-Aspergillus fumigatuselastase in sera of patients with aspergillosis (1994)

Anti-Aspergillus fumigatus alkaline protease IgG was investigated by Western blot. Specific IgG antibodies were detected in sera of two of nine patients with proven or highly probable invasive aspergillosis and in sera of one of eight patients with proven or highly probable allergic bronchopulmonary aspergillosis. No response was obtained in sera of 23 control patients. The specific but transient IgG response to this induced enzyme does not recommend its use as sole serodiagnostic aid.
STED nanoscopy of the centrosome linker reveals a CEP68-organized, periodic rootletin network anchored to a C-Nap1 ring at centrioles (2018)

The centrosome linker proteins C-Nap1, rootletin, and CEP68 connect the two centrosomes of a cell during interphase into one microtubule-organizing center. This coupling is important for cell migration, cilia formation, and timing of mitotic spindle formation. Very little is known about the structure of the centrosome linker. Here, we used stimulated emission depletion (STED) microscopy to show that each C-Nap1 ring at the proximal end of the two centrioles organizes a rootletin ring and, in addition, multiple rootletin/CEP68 fibers. Rootletin/CEP68 fibers originating from the two centrosomes form a web-like, interdigitating network, explaining the flexible nature of the centrosome linker. The rootletin/CEP68 filaments are repetitive and highly ordered. Staggered rootletin molecules (N-to-N and C-to-C) within the filaments are 75 nm apart. Rootletin binds CEP68 via its C-terminal spectrin repeat-containing region in 75-nm intervals. The N-to-C distance of two rootletin molecules is ∼35 to 40 nm, leading to an estimated minimal rootletin length of ∼110 nm. CEP68 is important in forming rootletin filaments that branch off centrioles and to modulate the thickness of rootletin fibers. Thus, the centrosome linker consists of a vast network of repeating rootletin units with C-Nap1 as ring organizer and CEP68 as filament modulator.
Fano interference between resonant and leaky waves in 1D silicon photonic crystal microcavities (2013)

Resonant integrated optical structures with spectra exhibiting asymmetric Fano line shapes are of interest for a variety of devices, including integrated sensors, electro-optic modulators and all-optical switches. Here we observe such line shapes in the transmission spectra of waveguide-loaded 1D photonic crystal (PC) microresonators, resulting from interference between the resonant transmission of the bus WG's fundamental quasi-TE mode, and leaky nonresonant transmission of a second-order quasi-TE mode through the PC region. The continuum state transmitted through the PC microcavity itself uniquely allows for devices requiring no additional waveguides or reflecting elements. Additionally, the devices are fabricated with 193-nm immersion photolithography in a CMOS memory process at Micron Technology, and though PC structures have previously been fabricated photolithographically, these are the first high-Q PC microcavity devices fabricated subject to the constraints and dielectric environment of a full electronics-capable CMOS process.
Electrostatic Formation of Quantum Dot/J-aggregate FRET Pairs in Solution (2009)

We report the formation and photonic properties of CdSe/ZnS quantum dot (QD)/J-aggregate donor−acceptor Forster resonant energy transfer (FRET) pairs that are electrostatically bound and dispersed in water. Assembly occurs when the positively charged dye, 1,1′,3,3′-tetraethyl-5,5′,6,6′-tetrachlorobenzimidazolocarbocyanine (TTBC), binds electrostatically to QDs that are coated with a negatively charged amphiphilic polymer. QD/J-aggregate FRET pairs display the broadband absorption in the visible and the ultraviolet (UV) part of the spectrum typical of quantum dots, along with the narrow emission linewidths characteristic of J-band emitters (∼12 nm full width at half-maximum). We use dynamic light scattering, transmission electron microscopy, photoluminescence spectroscopy, and photoluminescence lifetimes to conclude that the size of the aggregates formed in the presence of QDs is between 1−6 nm. We find the FRET radius of the QD/J-aggregate to be 5.1 nm. We further demonstrate electrostatic binding as a general synthetic strategy for these types of FRET pairs by attaching a negatively charged J-aggregate (BIC) to a quantum dot coated with positively charged ligands.