gebhart/patrepeval huggingface dataset:
Glycoproteomic Analysis of Serum from Patients with Gastric Precancerous Lesions (2013)

Gastric cancer is preceded by a carcinogenesis pathway that includes gastritis caused by Helicobacter pylori infection, chronic atrophic gastritis that may progress to intestinal metaplasia (IM), dysplasia, and ultimately gastric carcinoma of the more common intestinal subtype. The identification of glycosylation changes in circulating serum proteins in patients with precursor lesions of gastric cancer is of high interest and represents a source of putative new biomarkers for early diagnosis and intervention. This study applies a glycoproteomic approach to identify altered glycoproteins expressing the simple mucin-type carbohydrate antigens T and STn in the serum of patients with gastritis, IM (complete and incomplete subtypes), and control healthy individuals. The immunohistochemistry analysis of the gastric mucosa of these patients showed expression of T and STn antigens in gastric lesions, with STn being expressed only in IM. The serum glycoproteomic analysis using 2D-gel electrophoresis, Western blot, and MALDI-TOF/TOF mass spectrometry led to the identification of circulating proteins carrying these altered glycans. One of the glycoproteins identified was plasminogen, a protein that has been reported to play a role in H. pylori chronic infection of the gastric mucosa and is involved in extracellular matrix modeling and degradation. Plasminogen was further characterized and showed to carry STn antigens in patients with gastritis and IM. These results provide evidence of serum proteins displaying abnormal O-glycosylation in patients with precursor lesions of gastric carcinoma and include a panel of putative targets for the non-invasive clinical diagnosis of individuals with gastritis and IM.
Supplementary Figure from <sup>89</sup>Zr-panitumumab Combined With <sup>18</sup>F-FDG PET Improves Detection and Staging of Head and Neck Squamous Cell Carcinoma (2023)

Supplementary Figure from &lt;sup&gt;89&lt;/sup&gt;Zr-panitumumab Combined With &lt;sup&gt;18&lt;/sup&gt;F-FDG PET Improves Detection and Staging of Head and Neck Squamous Cell Carcinoma
Increased expression of CD11b/CD18 on phagocytes in ischaemic disease: a bridge between inflammation and coagulation (1997)

The aim of this study was to assess the expression of CD11b/CD18 integrin adhesion molecules on the phagocytes of patients with ischaemic diseases, and to evaluate the concentration of soluble adhesion molecules that are released from endothelium (sICAM-1) and from phagocytes (sL-selectin). A total of 370 patients were enrolled: 120 with coronary artery disease (CAD); 50 with peripheral artery occlusive disease (PAOD); and 200 control subjects with no clinical manifestations of ischaemic disease. CD11b/CD18 integrin was detected by flow cytometry, whereas sL-selectin and sICAM-1 concentrations were detected using a sandwich-type immunoassay. CD11b/CD18 integrin expression was found to be higher in the patients with ischaemic disease than in the control subjects (P < 0.001). The PAOD patients had higher values of CD11b/CD18 integrin than the CAD ones (P < 0.01). The concentration of soluble adhesion molecules did not show any significant differences within the three groups (P = NS). The high expression of CD11b/CD18 integrin in ischaemic disease patients may depend on the increased, but probably stable, cytokine network that has been demonstrated to occur in chronic ischaemic diseases: the difference observed between PAOD and CAD patients could be the consequence of higher inflammatory activation probably resulting from the greater extent of the atherosclerotic process in PAOD, or of the more localized ischaemic area in CAD patients. CD11b/CD18 can therefore be considered a marker of chronic phagocyte activation during ischaemic disease. On the other hand, sICAM and sL-selectin concentrations were found to be within the normal range; they have recently been considered as a marker for acute ischaemic events and acute inflammatory process activation. Our results confirm that in uncomplicated atherosclerosis no acute inflammatory process activation should occur.
Erratum: “Nonlinear frequency shift in Raman backscattering and its implications for plasma diagnostics” [Phys. Plasmas 23, 123104 (2016)] (2017)

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Archaeology of NIDDM: Excavation of the “Thrifty” Genotype (1991)

Since the 1940s, numerous cases of non-insulin-dependent diabetes mellitus (NIDDM) have been observed in certain American Indian populations. Extremely high prevalence rates of NIDDM occur most strikingly in several tribes of Paleo-Indians, whose ancestors migrated to North America greater than 11,000 yr ago. Archaeological evidence from that period indicates that certain groups of Paleo-Indians maintained an arctic-like hunter-gatherer life-style in an area in temperate North America ranging from Wyoming to Arizona. This life-style featured a reliance on unpredictable big game species as a major food source. However, at this time, big game species were becoming extinct. It is hypothesized that those Paleo-Indians who relied on big game as a food source developed a "thrifty" genotype that allowed a selective advantage during the periods of fasting that occurred between big game kills. It also is hypothesized that this thrifty genotype in these Indians may contribute to NIDDM when a sedentary life-style is adopted and food sources are constant. Because insulin resistance in muscle is a major feature of NIDDM, it is possible that insulin resistance per se is the phenotypic expression of the thrifty genotype.
Protected data storage system for optical discs (2003)

This paper presents a system that provides a data storage area on optical discs which is protected against unauthorized access. The protected area is referred to as a key locker. It is of particular importance to applications that use digital rights management (DRM). An advantage of the key locker concept is its DRM-agnostic nature. As such, any DRM system can benefit from the protected area.
Effects of ionizing radiation on DNA. Physical, chemical and biological aspects. (1978)

The publication presents the culmination of collaborative effort between specialists in the wide range of disciplines concerned with the effects of ionizing radiations on nucleic acids. Subjects discussed include: (1) structure and electronic properties of DNA; (2) radicals produced from nucleic acids; (3) transfer phenomena; (4) chemical changes; (5) and biological repair. Separate entries were made for the individual chapters.
Effects of electron-beam lithography on thin gate oxide reliability (2002)

In view of the rapid downscaling of design rules in CMOS technologies, current optical lithography tools are expected to be replaced with shorter wavelength lithography tools in the near future. One of the strong candidates for the next generation lithography tools is electron-beam (e-beam) lithography, in order to achieve the required fine geometry definition. However, e-beam irradiation of MOS structures can induce radiation damage, especially to the thin gate oxide. In this paper, the effects of e-beam lithography on thin gate oxide reliability are studied.
Operator for stroke interventions (2015)

The requisites of training for neuroendovascular procedures have been debated. A report by Jennifer Byrne was published in the July/August 2015 issue of Cardiology Today Intervention . In the report, ‘Acute stroke: a new target for endovascular therapy; experience and availability make interventional cardiologists uniquely qualified for acute stroke’, the author summarizes the findings of recent randomized controlled trials for endovascular treatment of acute ischemic stroke and then emphasizes the shortage of providers of neurointerventional stroke treatment. However, this is a controversial topic and many have suggested that too many neurointerventionalists are being trained in the USA.1 ,2 The report suggests that cardiologists should fill this perceived lack of neurointerventionalists by treating patients in small rural hospitals rather than sending them to a stroke center. We believe that this would be a giant leap backwards in quality and safety.

Treatment of strokes in small rural hospitals by individuals with limited training and experience and with support staff who are untrained in neurologic care seems unsafe. This idea undermines the hard work being done by hospitals that obtain both Primary and Comprehensive Stroke Center certifications, …
Analysis of autonomous deconfliction in Unmanned Aircraft Systems for Testing and Evaluation (2009)

Autonomous deconfliction capability is crucial to the successful deployment of unmanned aircraft systems (UAS) in most of their envisioned application scenarios. Civil and military applications of UAS demand ever-decreasing levels of human involvement and oversight, hence, UAS need to grow in autonomy. Autonomous deconfliction is a capability that is not only essential for the UAS's self-preservation, but also for avoiding damage to static infrastructure and/or to friendly and civilian aircraft flying contiguously. It is also key to the successful completion of the missions assigned to the UAS. Numerous solutions to partial aspects of autonomous deconfliction have been proposed. However, there is an enormous gap in systematic approaches that may be used for testing and evaluation (T&E) of autonomous capabilities such as deconfliction. This paper focuses on application of systems engineering-oriented tools to the analysis of autonomous deconfliction capability in UAS. The systems capability technical reference model (SC-TRM) presented in this work helps in identifying the different aspects of a deconfliction solution. Besides presenting the systems engineering-oriented tools and the analysis of the deconfliction problem based on those tools, this paper also proposes venues that may enable concrete implementation and development of T&E methods that are applicable to civil as well as military applications.
Antibody Binding Alters the Characteristics and Contents of Extracellular Vesicles Released by Histoplasma capsulatum (2016)

Histoplasma capsulatum produces extracellular vesicles containing virulence-associated molecules capable of modulating host machinery, benefiting the pathogen. Treatment of H. capsulatum cells with monoclonal antibodies (MAbs) can change the outcome of infection in mice. We evaluated the sizes, enzymatic contents, and proteomic profiles of the vesicles released by fungal cells treated with either protective MAb 6B7 (IgG1) or nonprotective MAb 7B6 (IgG2b), both of which bind H. capsulatum heat shock protein 60 (Hsp60). Our results showed that treatment with either MAb was associated with changes in size and vesicle loading. MAb treatments reduced vesicle phosphatase and catalase activities compared to those of vesicles from untreated controls. We identified 1,125 proteins in vesicles, and 250 of these manifested differences in abundance relative to that of proteins in vesicles isolated from yeast cells exposed to Hsp60-binding MAbs, indicating that surface binding of fungal cells by MAbs modified protein loading in the vesicles. The abundance of upregulated proteins in vesicles upon MAb 7B6 treatment was 44.8% of the protein quantities in vesicles from fungal cells treated with MAb 6B7. Analysis of orthologous proteins previously identified in vesicles from other fungi showed that different ascomycete fungi have similar proteins in their extracellular milieu, many of which are associated with virulence. Our results demonstrate that antibody binding can modulate fungal cell responses, resulting in differential loading of vesicles, which could alter fungal cell susceptibility to host defenses. This finding provides additional evidence that antibody binding modulates microbial physiology and suggests a new function for specific immunoglobulins through alterations of fungal secretion. IMPORTANCE Diverse fungal species release extracellular vesicles, indicating that this is a common pathway for the delivery of molecules to the extracellular space. However, there has been no study reporting the impact of antibody binding to the fungal cell on extracellular vesicle release. In the present work, we observed that treatment of H. capsulatum cells with Hsp60-binding MAbs significantly changed the size and cargo of extracellular vesicles, as well as the enzymatic activity of certain virulence factors, such as laccase and phosphatase. Furthermore, this finding demonstrates that antibody binding can directly impact protein loading in vesicles and fungal metabolism. Hence, this work presents a new role for antibodies in the modification of fungal physiology.
Histogram preserving image transformations (2002)

Histograms are used to analyze and classify images. They have been found experimentally to have low sensitivity to certain types of image morphisms, for example, viewpoint changes and object deformations. However the precise effect of these image morphisms on the histogram has not been studied. In this work we derive the complete class of local transformations that preserve the histogram or simply scale its magnitude. To achieve this the transformations are represented as solutions to families of vector fields acting on the image. It is then shown that weak perspective projection and paraperspective projection belong to this class and simply scale the histogram. The results on weak perspective projection, together with the effect of illumination, are used to compute the histogram of the projection of 3D polyhedral objects. We verify the analytical results with several examples. Moreover we present and test a system that recognizes and approximates the poses of 3D polyhedral objects independent of viewpoint.
Tenfold topology of crystals: Unified classification of crystalline topological insulators and superconductors (2021)

The celebrated tenfold way of Altland-Zirnbauer symmetry classes discern any quantum system by its pattern of nonspatial symmetries. It lays at the core of the periodic table of topological insulators and superconductors which provided a complete classification of weakly interacting electrons' noncrystalline topological phases for all symmetry classes. Over recent years, a plethora of topological phenomena with diverse surface states has been discovered in crystalline materials. In this paper, we obtain an exhaustive classification of topologically distinct ground states as well as topological phases with anomalous surface states of crystalline topological insulators and superconductors for key space-groups, layer-groups, and rod-groups. This is done in a unified manner for the full tenfold way of Altland-Zirnbauer nonspatial symmetry classes. We establish a comprehensive paradigm that harnesses the modern mathematical framework of equivariant spectra; it allows us to obtain results applicable to generic topological classification problems. In particular, this paradigm provides efficient computational tools that enable an inherently unified treatment of the full tenfold way.
Prognostic Value of Incremental Lactate Elevations in Emergency Department Patients With Suspected Infection (2012)

In ED patients with suspected infection, we found a curvilinear relationship between incremental elevations in lactate concentration and mortality. These data support the use of lactate as a continuous variable rather than a categorical variable for prognostic purposes.
Joint international consensus statement for ending stigma of obesity (2020)

People with obesity commonly face a pervasive, resilient form of social stigma. They are often subject to discrimination in the workplace as well as in educational and healthcare settings. Research indicates that weight stigma can cause physical and psychological harm, and that affected individuals are less likely to receive adequate care. For these reasons, weight stigma damages health, undermines human and social rights, and is unacceptable in modern societies. To inform healthcare professionals, policymakers, and the public about this issue, a multidisciplinary group of international experts, including representatives of scientific organizations, reviewed available evidence on the causes and harms of weight stigma and, using a modified Delphi process, developed a joint consensus statement with recommendations to eliminate weight bias. Academic institutions, professional organizations, media, public-health authorities, and governments should encourage education about weight stigma to facilitate a new public narrative about obesity, coherent with modern scientific knowledge.
A reconstruction algorithm for temporally aliased seismic signals recorded by the InSight Mars lander (2020)

The NASA InSight lander successfully placed a seismometer on the surface of Mars. Alongside, a hammering device was deployed that penetrated into the ground to attempt the first measurements of the planetary heat flow of Mars. The hammering of the heat probe generated repeated seismic signals that were registered by the seismometer and can potentially be used to image the shallow subsurface just below the lander. However, the broad frequency content of the seismic signals generated by the hammering extends beyond the Nyquist frequency governed by the seismometer's sampling rate of 100 samples per second. Here, we propose an algorithm to reconstruct the seismic signals beyond the classical sampling limits. We exploit the structure in the data due to thousands of repeated, only gradually varying hammering signals as the heat probe slowly penetrates into the ground. In addition, we make use of the fact that repeated hammering signals are sub-sampled differently due to the unsynchronised timing between the hammer strikes and the seismometer recordings. This allows us to reconstruct signals beyond the classical Nyquist frequency limit by enforcing a sparsity constraint on the signal in a modified Radon transform domain. Using both synthetic data and actual data recorded on Mars, we show how the proposed algorithm can be used to reconstruct the high-frequency hammering signal at very high resolution. In this way, we were able to constrain the seismic velocity of the top first meter of the Martian regolith.
Characterization of the rat colonic aldosterone receptor and its activation process. (1986)

Aldosterone increases sodium absorption, short circuit current, and transmural potential difference in rat colon. We studied the rat colonic aldosterone receptor using the synthetic glucocorticoid, 11 beta, 17 beta-dihydroxy-17 alpha-propynylandrosta-1,4,6-triene-3-one, to prevent binding to the glucocorticoid receptor. Specific aldosterone binding was found in proximal and distal colon. Heating to 25 degrees C decreased binding within 15 min, but the protease inhibitor, phenylmethylsulfonyl fluoride, stabilized binding. Binding was highest in terminal distal colon. Competitive binding assay showed aldosterone specificity compared to other competitors was greater at 30 than at 4 degrees C, suggesting temperature-sensitive changes in receptor specificity. Scatchard analysis revealed a straight line with a KD of 2.5 nM at 0 degrees C and 4.1 nM at 30 degrees C. Bmax was higher in distal than in proximal colon (30 degrees C, 156 +/- 33 versus 65 +/- 9 fmol/mg protein) and increased by 36% in proximal and 180% in distal colon at 30 degrees C compared to 0 degrees C. DEAE-cellulose chromatography of unactivated receptor demonstrated a single peak eluting at 200-250 mM KCl. Heat, ATP, and gel filtration did not activate the receptor, whereas increasing cytosolic salt concentration to 300 mM KCl, raising the pH to 8, or adding EGTA and EDTA caused increased DNA-cellulose binding and a new peak eluting at 30-80 mM KCl on DEAE-cellulose chromatography. There is a specific aldosterone receptor in colon with increasing number of binding sites from proximal to most distal segments paralleling aldosterone's physiological effects. Absence of receptor activation with heat, gel filtration, or ATP suggests differences between activation of the aldosterone receptor and other steroid hormone receptors.
Early life stage toxicity of extracts from the African fish poison plants Tephrosia vogelii Hook. f. and Asystasia vogeliana Benth. on zebrafish embryos (2004)

Embryos of Danio rerio are highly susceptible to extracts of the plants Tephrosia vogelii and Asystasia vogeliana . The concentration of the dried extracts at which 50% of the embryos were affected (EC 50 ) after 24 h exposure were 320 and 572 μg l −1 , respectively; corresponding 50% mortality (LC 50 ) values after 48 h exposure were 493 and 869 μg l −1 . Results indicate that the use of these ichthyotoxic plants might have a severe impact on the survival of fish larvae in the field.
Multi-agent Deep Reinforcement Learning for Shock Wave Detection and Dissipation using Vehicle-to-Vehicle Communication (2022)

Traffic shock waves are a commonly occurring phenomena caused by the delays in reaction times of Human Driven Vehicles (HDVs) resulting in unnecessary congestion in highway networks. Application of a suitable moving bottleneck control using Connected Autonomous Vehicles (CAVs) can result in shock wave mitigation and smoothing of the traffic flow. This traffic control scheme is dependent on accurately predicting shock wave conditions while choosing the best control to apply for the observation available to the CAV. In this work, we propose the use of a multi-agent shared policy reinforcement learning algorithm which leverages communication between CAVs for improved observability of downstream traffic conditions. A key feature of this method is the ability to perform shock wave dissipation control without the need for global information and the applicability of this method to multi-lane mixed traffic highways of arbitrary structure. We use the shared-parameter Proximal Policy Optimization (PPO) reinforcement learning strategy for obtaining the controls for each CAV in the simulation. We also built a custom SUMO-Gym wrapper for the multi-lane highway simulation with custom designed observation space, action space and rewards for each agent. The shock wave dissipation efficiency is evaluated on a three lane circular highway loop using realistic traffic simulation software and low CAV penetration levels.
Development of self-tuned diamond milling system for fabricating infrared micro-optics arrays with enhanced surface uniformity and machining efficiency (2019)

Infrared micro-optics arrays (MOAs) featuring large numbers of micro-freeform lenslet are required increasingly in advanced infrared optical systems. Ultra-precision diamond cutting technologies have been widely used to fabricate MOAs with high form accuracy. However, the existing technologies can easily cause the non-uniformly fractured surface of infrared MOAs, due to the inherent low fracture toughness and high anisotropy of infrared materials as well as the time-varying chip thickness induced by ever-changing height and slope of the desired MOAs. In this study, a novel self-tuned diamond milling (STDM) system is proposed to achieve the ductile cutting of infrared MOAs with enhanced the surface uniformity and machining efficiency, and the corresponding toolpath planning algorithm is developed. In STDM system, a dual-axial fast servo motion platform is integrated into a raster milling system to self-adaptively match the maximum chip thickness for each tool rotational cycle with the critical depth of cut of the infrared material according to the local surface topography, thereby obtaining crack-free lenslet with high surface uniformity. Practically, micro-aspheric MOAs free from fractures are successfully machined on single-crystal silicon, a typical infrared material, to validate the proposed cutting concept. Compared with the conventional diamond milling, the proposed STDM is demonstrated to be able to avoid the non-uniform fractures without needing to reduce feed rate, and a smaller surface roughness of 4 nm and nearly double machining efficiency are achieved.