gebhart/patrepeval huggingface dataset:
Screening for Lung Cancer with Low-Dose Spiral Computed Tomography (2002)

Studies suggest that screening with spiral computed tomography can detect lung cancers at a smaller size and earlier stage than chest radiography can. To evaluate low-radiation-dose spiral computed tomography and sputum cytology in screening for lung cancer, we enrolled 1,520 individuals aged 50 yr or older who had smoked 20 pack-years or more in a prospective cohort study. One year after baseline scanning, 2,244 uncalcified lung nodules were identified in 1,000 participants (66%). Twenty-five cases of lung cancer were diagnosed (22 prevalence, 3 incidence). Computed tomography alone detected 23 cases; sputum cytology alone detected 2 cases. Cell types were: squamous cell, 6; adenocarcinoma or bronchioalveolar, 15; large cell, 1; small cell, 3. Twenty-two patients underwent curative surgical resection. Seven benign nodules were resected. The mean size of the non-small cell cancers detected by computed tomography was 17 mm (median, 13 mm). The postsurgical stage was IA, 13; IB, 1; IIA, 5; IIB, 1; IIIA, 2; limited, 3. Twelve (57%) of the 21 non-small cell cancers detected by computed tomography were stage IA at diagnosis. Computed tomography can detect early-stage lung cancers. The rate of benign nodule detection is high.
ACE2 in tumor cells and tumor vasculature: Negligible intercellular transfer from cancer cells into endothelial cells (2021)

Cancer patients are more susceptible to severe coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Angiotensin-converting enzyme 2 (ACE2) is the functional host receptor for SARS-CoV-2 entering into human cells. Bioinformatics’ analyses have revealed that ACE2 is upregulated in some cancer cells. In the present study, we evaluated ACE2 protein expression levels in several common malignancies compared to non-cancerous normal tissues. ACE2 expression was elevated in colorectal adenocarcinoma, pancreatic adenocarcinoma, gastric adenocarcinoma, and papillary renal cell carcinoma cancer. Yet, it was suppressed in chromophobe renal cell carcinoma, testicular germ cell tumors, and papillary thyroid carcinoma. Two tumor tissue microarrays were used to evaluate the prognostic value of ACE2 expression in patients with gastric adenocarcinoma, and colorectal adenocarcinoma without COVID-19. No significant survival benefit was found for patients with overexpression of ACE2 in the tumor. In the tumor vasculature, ACE2 expression was observed in only 54% of the tumor micro-vessels. Using an in vitro co-culture of endothelial cells and tumor cells overexpressing fusion protein ACE2-red fluorescent protein, we did not observe any clear and convincing intercellular transfer of ACE2 from cancer cells into endothelial cells. In summary, alteration of ACE2 expression was found in common malignancies, but there is no evidence of intercellular transfer of ACE2 from cancer cells to endothelial cells.
Design, synthesis and evaluation of 2-deoxy-2-iodovinyl-branched carbohydrates as potential brain imaging agents (1986)

Radioiodinated carbohydrates such as 2-deoxy-2-iodo-D-glucose and 3-deoxy-3-iodo-D-glucose undergo facile chemical or in vivo deiodination which precludes their use as radiotracers of glucose metabolism in tissues. To overcome the problems resulting from in vivo deiodination, we explored the concept of stabilizing radioiodide on a model carbohydrate, (E)-C-3-iodovinyl-D-allose (10) as an iodovinyl moiety. This agent did not exhibit brain specificity but showed low in vivo deiodination which demonstrated for the first time that radioiodide can be stabilized on a carbohydrate. The goal of this study was to develop a deoxy-branched carbohydrate with radioiodide stabilized as a vinyliodide with the objective of achieving high brain uptake. 10 refs., 1 fig., 1 tab.
Effect of ammonification temperature on the formation of coaxial GaN/Ga<sub>2</sub>O<sub>3</sub>nanowires (2016)

The effect of ammonification temperature on the formation of coaxial GaN/Ga2O3 nanowires from β-Ga2O3 nanowires is reported in this work. High quality wurtzite GaN material showing a single c-plane phase is achieved from β-Ga2O3 nanowires having monoclinic crystal structure at a high ammonification temperature of 1050 °C. Lower ammonification temperatures such as 900 °C are also adequate for achieving coaxial GaN/Ga2O3 nanowire heterostructures, and the degree of GaN phase can be adjusted by varying the ammonification temperature. The crystalline quality of GaN/Ga2O3 nanowires improves with increasing the ammonification temperature. Resonant Raman spectra of GaN/Ga2O3 nanowires show Raman progression through multiple longitudinal-optical-phonon modes with overtones of up to second order. The development and improvement of the emission peak toward the near band edge of GaN at different ammonification temperatures were investigated using cathodoluminescence and photoluminescence characterization.
Addition of GeO <sub>2</sub> to Reduce the Viscosity of Parent Glasses for Low‐Expansion, Transparent Glass–Ceramics Containing High‐Quartz Solid Solutions (2006)

Parent glasses for fabricating glass–ceramics with nanometer‐sized crystals usually have high viscosities, resulting in high processing temperatures. In this study, GeO 2 was added to a transparent, near‐zero thermal‐expansion Li 2 O–Al 2 O 3 –SiO 2 glass–ceramic to reduce the viscosity of the parent glass. The effects of this compositional modification on the viscosity and crystal‐nucleation rate of the parent glasses, and on the crystal size, thermal expansion, and optical transparency of the resulting glass–ceramics were investigated. It was found that addition of GeO 2 was useful in reducing the glass viscosity. Owing to the reduced nucleating rate with the increase in the GeO 2 content, the nucleating times required for reaching the smallest crystal size, the lowest coefficient of thermal expansion, and the highest transparency were all increased. With increasing GeO 2 content, the lowest coefficient of thermal expansion that can be reached for glass–ceramics increased (0.14–2.9 × 10 −6 K −1 ). The highest transparency of the GeO 2 ‐containing glass–ceramics is almost as good as that of the GeO 2 ‐free glass–ceramic and is almost independent of GeO 2 content when the crystal size is smaller than about 65 nm.
Bulky Phosphane Ligand for Monoselective Ruthenium-Catalyzed, Directed o-C–H Arylation with Challenging Aryl Chlorides (2016)

Functionalized aryl chlorides are more economically attractive but usually much more difficult as substrates in metal-mediated couplings than the corresponding bromides and iodides. A catalyst prepared from a bulky (biaryl)diphenyl phosphane and a common ruthenium source (1:1) mediates selective direct monoarylations of arenes bearing 2-pyridyl and related <i>ortho</i>-directing groups in good yields. Sequential arylations to heterodiarylated products also proceed in satisfactory yields.
Dual-frequency patch antennas (1997)

Dual-frequency patch antennas may provide an alternative to large-bandwidth planar antennas, in applications in which large bandwidth is really needed for operating at two separate transmit-receive bands. When the two operating frequencies are far apart, a dual-frequency patch structure can be conceived to avoid the use of separate antennas. In this paper, a critical overview of possible solutions for dual-frequency patch antennas is presented, and future perspectives are outlined. Geometries are discussed in particular.
Microservices: Architecting for Continuous Delivery and DevOps (2018)

Businesses today need to respond to customer needs at unprecedented speeds. Driven by this need for speed, many companies are rushing to the DevOps movement and implementing Continuous Delivery (CD). I had been implementing DevOps and CD for Paddy Power, a multi-billion-euro betting and gaming company, for four years. I had found that software architecture can be a key barrier. To address the architectural challenges, we tried an emerging architectural style called Microservices. I have observed increased deployability, modifiability, and resilience to design erosion. At the same time, I also observed new challenges associated with the increased number of services, evolving contracts among services, technology diversity, and testing. I share the practical strategies that can be employed to address these new challenges, discuss situations for which Microservices may not be a good choice, and outline areas that require further research.
Lignin and Lignans (2010)

Over the past four decades, there has been immense progress in every area of lignin science, ranging from the enzymology of lignin biodegradation, to the delignification of wood fiber during pulping and bleaching, to advances in spectroscopy. Lignin and Lignans: Advances in Chemistry captures the developments that have been achieved by world-class
Hydrogen-Bonding and Hydrophobic Groups Contribute Equally to the Binding of Hyperactive Antifreeze and Ice-Nucleating Proteins to Ice (2019)

Hyperactive insect antifreeze proteins and bacterial ice-nucleating proteins are arguably the most potent ice-binding molecules in nature. These highly effective proteins bind ice through amphiphilic ice-binding sites based on arrays of threonine residues. It remains poorly understood how hydrophilic and hydrophobic groups of the binding site contribute to the ice affinity of proteins. Here, we use molecular simulations to demonstrate that the hydrogen-bonding and hydrophobic groups at the ice-binding site of the antifreeze protein TmAFP of Tenebrio molitor and extended ice-nucleating protein surfaces contribute distinctively yet almost equally in magnitude to their binding free energy to ice. The methyl groups rigidize the ice-binding site, slow the water dynamics at the ice-binding surface, and stabilize the clathrate-like water in the anchored clathrate motif that binds these proteins to ice. We find that hydrophobic dehydration of the methyl group does not contribute to the binding free energy of the protein to ice. The role of the hydroxyl groups is to anchor the clathrate-like water through direct hydrogen-bonding, positioning and slowing the dynamics of water at the trough of the binding site. We uncover a correlation between slower dynamics of water at the binding site for the protein in solution and stronger free energy of binding of the protein to ice. The synergy between hydrophobic and hydrophilic groups unveiled by this study provides guidance for the design of synthetic ice-binding molecules with enhanced ice nucleation and antifreeze activity.
Histone variants: essential actors in male genome programming (2017)

Prior to its transmission to the offspring, the male genome has to be tightly compacted. A genome-scale histone eviction and the subsequent repackaging of DNA by protamines (Prms) direct this essential genome condensation step. The requirement for male germ cells to undergo such a dramatic and unique genome reorganization explains why these cells express the largest number of histone variants, including many testis-specific ones. Indeed, an open chromatin, nucleosome instability and a facilitated process of histone disassembly are direct consequences of the presence of these histone variants in the chromatin of male germ cells. These histone-induced changes in chromatin first control a stage-specific gene expression program and then directly mediate the histone-to-Prm transition process. This review aims at summarizing and discussing a series of recent functional studies of male germ cell histone variants with a focus on their impact on the process of histone eviction and male genome compaction.
Positive Feedback Activation of Estrogen Receptors by the CXCL12-CXCR4 Pathway (2009)

Induction of estrogen-regulated gene transcription by estrogen receptors ERalpha and ERbeta plays an important role in breast cancer development and growth. High expression of the chemokine receptor CXCR4 and its ligand CXCL12/stromal cell-derived factor 1 (SDF-1) has also been correlated with aggressive breast tumor phenotypes. Here, we describe a positive regulatory loop between the CXCR4/SDF-1 signaling pathway and ER transcriptional competence in human breast cancer cells. Treatment of breast carcinoma MCF-7 cells with SDF-1 increased ER transcriptional activity and expression of ER target genes, including SDF-1 itself. These effects were blocked by the antiestrogen ICI-182780 and by CXCR4 silencing and, conversely, estrogen-induced gene expression and growth of MCF-7 cells were impaired on CXCR4 inhibition. Both ERalpha and ERbeta were activated by SDF-1 in the presence of CXCR4 and by overexpression of a constitutively active CXCR4, indicating that CXCR4 signals to both receptors. In particular, ERbeta was able to translate the effects of SDF-1 on its own expression, as well as enhance activator protein 1 (AP-1) containing genes cyclin D1 and c-Myc in the presence of tamoxifen. This correlated with an increased ERbeta occupancy of responsive promoters at both estrogen-responsive and AP-1 elements. Ser-87, a conserved mitogen-activated protein kinase site in ERbeta, was highly phosphorylated by SDF-1, revealing an essential role of the AF-1 domain in response to CXCR4 activation. These results identify a complete autocrine loop between the CXCR4/SDF-1 and ERalpha/ERbeta signaling pathways that dictates ER-dependent gene expression and growth of breast cancer cells.
CuckooFlow: Achieving Fast Packet Classification for Virtual OpenFlow Switching by Exploiting Network Traffic Locality (2019)

The growing trend of network virtualization leads to a widespread deployment of virtual switches in virtualized environments. However, virtual switching is confronted with great performance challenges regarding packet classification especially in OpenFlow-based software defined networks. This paper takes an insight into network traffic locality from the perspective of exact flows and wildcard flows, and propose a fast packet classification scheme CuckooFlow. In particular, we devise an active exact flow cache with cuckoo hashing to predict the respective flow entry for each arrived packet. Subsequently, we formulate its cache hit rate based on packet-in-batch arrivals, and average search length of the packet classification scheme. Finally, our proposed CuckooFlow scheme is evaluated with real network traffic traces by experiments. The experimental results indicate that our proposed scheme outperforms traditional ones Open vSwitch and CuckooDistributor in terms of cache hit rates and average search length, and contributes to promote virtual OpenFlow switching performance.
High efficiency silicon and Germanium stack junction solar cells (2012)

We have fabricated Si/Ge stack junction solar cells in order to overcome silicon single junction limit efficiency. Ge cell can absorb long wavelength photons that cannot be absorbed in Si. Bottom Ge solar cell can theoretically yield additional 5% efficiency to Si top cell. We have fabricated 21.3% top Si / 1.6% bottom Ge stack junction with 22.9% module efficiency. SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and SiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> double insulating interlayers were optimized in order to transmit long wavelength photon to the Ge cell and achieve good passivation at the interlayer. The stack junction will be able to overcome the Si practical efficiency limit of 26% in the near future, and be the candidate for the next generation crystalline Si solar cell.
COVID‑19: An update of current knowledge (Review) (2021)

There is a current public health issue threatening human health worldwide with the rapid spread of the novel coronavirus (2019‑nCoV) or severe acute respiratory syndrome coronavirus‑2 (SARS‑CoV‑2). The infection was reported to first originate in bats and subsequently spread to humans via yet unknown source animals in Wuhan, Hubei, China in December, 2019. Coronavirus disease 2019 (COVID‑19) caused by extreme acute respiratory coronavirus‑2 syndrome (SARS‑CoV‑2) is an unprecedented healthy global emergency. The outbreak of SARS‑CoV‑2 has once again revealed the vulnerabilities of global healthcare systems, the capacity of these systems to respond to an infectious threat, as well as the rate of infection and transmission across international borders. The present review article aimed to provide an update of the current knowledge regarding COVID‑19 epidemiology, pathogenesis and transmission, as well as public health measures. The present review also emphasises the key learning points related to COVID‑19 prevention and identifies the need to invest in healthcare systems, community‑led defence systems, as well as the need for resilience and global health security.
Time and frequency domain analysis of EEG signals for seizure detection: A review (2016)

Electroencephalography is non-invasive tool used in monitoring brain activities and diagnosis of many neurological disorders. EEG is a measurement tool to measure electrical activity generated by translating chemical variation in brain into voltage. EEG signals are measured with multi-electrode placed at properly localized part of the brain with either intracranial or Scalp EEG method. EEG (Electroencephalograph) analysis has become very important to detect various human diseases. The most important and simple aspect in processing EEG signals is to use time frequency analysis for possible diagnosis. Advanced methods of spectral analysis can extract new information encompassed in EEG signals by means of specific parameters. The EEG analysis plays very important role in feature extraction of EEG signal for detecting and predicting various brain diseases. The main objective of this paper is to study time-frequency analysis of EEG signal and compare their performances.
Macromolecular crowding amplifies adipogenesis of human bone marrow-derived MSCs by enhancing the pro-adipogenic microenvironment (2014)

The microenvironment plays a vital role in both the maintenance of stem cells in their undifferentiated state (niche) and their differentiation after homing into new locations outside this niche. Contrary to conventional in-vitro culture practices, the in-vivo stem cell microenvironment is physiologically crowded. We demonstrate here that re-introducing macromolecular crowding (MMC) at biologically relevant fractional volume occupancy during chemically induced adipogenesis substantially enhances the adipogenic differentiation response of human bone marrow-derived mesenchymal stem cells (MSCs). Both early and late adipogenic markers were significantly up-regulated and cells accumulated 25-40% more lipid content under MMC relative to standard induction cocktails. MMC significantly enhanced deposition of extracellular matrix (ECM), notably collagen IV and perlecan, a heparan sulfate proteoglycan. As a novel observation, MMC also increased the presence of matrix metalloproteinase-2 in the deposited ECM, which was concomitant with geometrical ECM remodeling typical of adipogenesis. This suggested a microenvironment that was richer in both matrix components and associated ligands and was conducive to adipocyte maturation. This assumption was confirmed by seeding undifferentiated MSCs on decellularized ECM deposited by adipogenically differentiated MSCs, Adipo-ECM. On Adipo-ECM generated under crowding, MSCs differentiated much faster under a classical differentiation protocol. This was evidenced throughout the induction time course, by a significant up-regulation of both early and late adipogenic markers and a 60% higher lipid content on MMC-generated Adipo-ECM in comparison to standard induction on tissue culture plastic. This suggests that MMC helps build and endow the nascent microenvironment with adipogenic cues. Therefore, MMC initiates a positive feedback loop between cells and their microenvironment as soon as progenitor cells are empowered to build and shape it, and, in turn, are informed by it to respond by attaining a stable differentiated phenotype if so induced. This work sheds new light on the utility of MMC to tune the microenvironment to augment the generation of adipose tissue from differentiating human MSCs.
SARS病毒蛋白质的质谱表征：初步报告* s (2003)

一种新的冠状病毒被牵连是严重急性呼吸综合征（SARS）的致病剂。我们已经使用来自几个SARS患者的康复血清，从暴露于灌洗的细胞中检测培养物上清液中的蛋白质。通过基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）作为〜46-KDA物种来鉴定上清液中最突出的蛋白质。发现这是一种新的核衣壳蛋白，几乎恰好地匹配了在最近公开的同一病毒分离物的核苷酸序列中预测的一个预测的蛋白质（>96％的覆盖范围）。通过MALDI-TOF MS（42％覆盖率）检查了对应于预测的~139-kDa穗糖蛋白的第二病毒蛋白。在肽N-糖苷酶F消化后，确认该蛋白质中的12位糖基化位点。还鉴定了附着于四个位点的糖。这些结果表明，核衣壳蛋白是可能对早期诊断有用的主要免疫原性，并且穗糖蛋白可能在对抗SARS中的预防性介入的特别有吸引力的靶标。
Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS (2017)

3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg<sup>2+</sup>. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg<sup>2+</sup> is still elusive. Therefore, mechanistic role played by Mg<sup>2+</sup> in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg<sup>2+</sup> have shown entry of Mg<sup>2+</sup> from bulk solvent into active site. Presence of Mg<sup>2+</sup> in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg<sup>2+</sup> into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a "lid" covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg<sup>2+</sup> suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors.
Medical imaging by fluorescent x-ray CT: its preliminary clinical evaluation (2002)

Fluorescent x-ray CT (FXCT) with synchrotron radiation (SR) is being developed to detect the very low concentration of specific elements. The endogenous iodine of the human thyroid and the non-radioactive iodine labeled BMIPP in myocardium were imaged by FXCT. FXCT system consists of a silicon (111) double crystal monochromator, an x-ray slit, a scanning table for object positioning, a fluorescent x-ray detector, and a transmission x-ray detector. Monochromatic x-ray with 37 keV energy was collimated into a pencil beam (from 1 mm to 0.025 mm). FXCT clearly imaged endogenous iodine of thyroid and iodine labeled BMIPP in myocardium, whereas transmission x-ray CT could not demonstrate iodine. The distribution of iodine was heterogeneous within thyroid cancer, and its concentration was lower than that of normal thyroid. Distribution of BMIPP in normal rat myocardium was almost homogeneous; however, reduced uptake was slightly shown in ischemic region. FXCT is a highly sensitive imaging modality to detect very low concentration of specific element and will be applied to reveal endogenous iodine distribution in thyroid and to use tracer study with various kinds of labeled material.