gebhart/patrepeval huggingface dataset:
Salivary protein expression profiles of five species of Pentatomidae (Hemiptera) (2023)

Abstract Stink bug (Hemiptera: Pentatomidae) development typically requires feeding on a diversity of plant species and various plant tissues. During feeding, stink bugs discharge salivary enzymes with roles in extraoral digestion and countering plant defense responses. Although previous research has described digestive salivary proteins from stink bugs, less is known of the salivary proteins involved in the suppression of plant defenses. We sequenced the transcriptomes of salivary glands dissected from five stink bug species collected from non-crop habitats in Washington: Halyomorpha halys (Stål), Nezara viridula L., Euschistus conspersus (Uhler), Thyanta pallidovirens (Stål), and Chlorochroa ligata (Say). We identified a total of 677 candidate secreted proteins from the salivary glands of the five species. Based on work from other insects, many of the proteins have potential functions in the suppression of plant defense signaling and deactivation of plant defense molecules. We also identified salivary proteins with potential roles in the extraoral digestion of plant tissues, protection from entomopathogens, and deposition of salivary sheaths. This report provides a curation of putative salivary effector genes for further functional analysis.
Emergence of drug-resistant HIV-1 variants in patients undergoing structured treatment interruptions (2002)

We report the emergence of drug-resistant viral mutations in chronically HIV-infected individual undergoing structured treatment interruptions (STI). THe protease mutations K101E and K103N were detected at the end of the second or third STI. We concluded that the repeated abrupt termination and resumption of certain antiretroviral drug regimens during STI therapy may lead to the development of drug resistance in chronically HIV-infected individuals.
SEROPREVALENCE OF ANTI-MANNOSE BINDING LECTIN AUTOANTIBODIES IN PATIENTS WITH RHEUMATOID ARTHRITIS IN SANA'A CITY- YEMEN (2018)

Objective: Rheumatoid arthritis (RA) characterized by synovial inflammation and destruction of cartilage and bone. Until now there is no single test that diagnoses RA, however, several blood tests may suggest the presence of this disease. RA is associated with the presence of a number of autoantibodies as such as rheumatoid factor (RF), anti-cyclic citrullinated peptide (ACPA) and anti-mannose binding lectin (anti-MBL). This study aimed firstly to investigate the presence of anti-MBL autoantibodies in the sera of RA patients and healthy controls and secondly to determine the diagnostic value of this marker in comparison with the classical RF, C- reactive protein (CRP) and ACPA among RA cases. Methods: This case-control study was conducted at four health establishments; two public (Al-Thawra Modern General Hospital and National Center of Central Public Health Laboratories) and two private (University of Science and Technology Hospital and Aulqi Specialized Medical Laboratories) in Sana'a city. Ninety-four individuals were enrolled in this study. Forty-seven persons were clinically diagnosed to have RA by a rheumatologist and 47 healthy subjects without RA were used as controls. Sera were separated and tested for presence of serum anti-MBL autoantibodies, ACPA, RF and CRP by a commercially available enzyme linked immunosorbent assay (ELISA) and latex agglutination technique. Results: Study results showed that the mean±SD for the levels of serum anti-MBL autoantibodies among RA cases were 394±243 ng/ml which were significantly higher than that recorded among healthy controls (217±173 ng/ml). The levels of serum anti-MBL autoantibodies were associated with positive RF and CRP tests (p=.02 and .007 respectively), but not with positive ACPA test (p=.42). Conclusion: The result of this study showed higher levels of serum anti-MBL autoantibodies among RA cases comparing with the healthy controls and reveal an association with positive results for RF and CRP, but not with ACPA. Therefore, the anti-MBL antibody levels may associated with systemic autoimmune diseases and might not exclusive to RA. Peer Review History: Received 8 March 2018; Revised 12 April; Accepted 1 May, Available online 15 May 2018 Received file: Reviewer's Comments: Average Peer review marks at initial stage: 6.5/10 Average Peer review marks at publication stage: 8.0/10 Reviewer(s) detail: Dr. Ahmad Abdelsattar El-Ebiary, Tanta University Hospitals, Tanta, Egypt, a.ebiary@med.tanta.edu.eg Dr. Anthony C. C. Egbuonu, Michael Okpara University of Agriculture, Nigeria, tonycemalukegbuonu@yahoo.com Similar Articles: PREVALENCE OF DYSLIPIDEMIA AND ITS ASSOCIATION WITH DISEASE ACTIVITY IN PATIENTS WITH RHEUMATOID ARTHRITIS IN SULAIMANI GOVERNORATE THE ASSOCIATION OF EPSTEIN-BARR VIRUS ANTIBODIES WITH RHEUMATOID ARTHRITIS AMONG YEMENI PATIENTS IN SANA’A CITY INTERLEUKIN-22 SERUM LEVELS IN PATIENTS WITH RHEUMATOID ARTHRITIS IN SANA'A CITY, YEMEN
Shining new light on sensory brain activation and physiological measurement in seals using wearable optical technology (2021)

Sensory ecology and physiology of free-ranging animals is challenging to study but underpins our understanding of decision-making in the wild. Existing non-invasive human biomedical technology offers tools that could be harnessed to address these challenges. Functional near-infrared spectroscopy (fNIRS), a wearable, non-invasive biomedical imaging technique measures oxy- and deoxyhaemoglobin concentration changes that can be used to detect localized neural activation in the brain. We tested the efficacy of fNIRS to detect cortical activation in grey seals (<i>Halichoerus grypus</i>) and identify regions of the cortex associated with different senses (vision, hearing and touch). The activation of specific cerebral areas in seals was detected by fNIRS in responses to light (vision), sound (hearing) and whisker stimulation (touch). Physiological parameters, including heart and breathing rate, were also extracted from the fNIRS signal, which allowed neural and physiological responses to be monitored simultaneously. This is, to our knowledge, the first time fNIRS has been used to detect cortical activation in a non-domesticated or laboratory animal. Because fNIRS is non-invasive and wearable, this study demonstrates its potential as a tool to quantitatively investigate sensory perception and brain function while simultaneously recording heart rate, tissue and arterial oxygen saturation of haemoglobin, perfusion changes and breathing rate in free-ranging animals. This article is part of the theme issue 'Measuring physiology in free-living animals (Part I)'.
Land Use Inference from Mobility Traces (2019)

We show how to infer land use from mobility traces. Instead of using manual surveys or aerial image interpretation, our research shows how to use mobility traces to infer the number of businesses and residences in each cell of a grid on the ground. Our mobility traces give the location of people at different times of day. Using mobility data from 1.8 million users, we build regression models that map from average hourly occupancy in a grid cell to the number of businesses and residences inside the cell. We show which hours of the day are most indicative of the contents of a cell.
Output Power and Loading of Superconducting Quantum Array (2014)

Using numerical simulation, we investigate the output power and loading tradeoffs for Superconducting Quantum Arrays (SQAs) suggested for the implementation of broadband radio-frequency systems, including active electrically small antennas capable of providing highly linear transfer characteristics with a high dynamic range. Standard matching loads used for linear microwave networks, including passive antennas, are not applicable for the active SQA-based circuits generally due to the strong shunting effect restricting the attainable linearity. At the same time, the output power of an active device can be increased by a power supply even for the impedance-mismatched circuits. Both the optimum achievable balance of the shunt effects and getting the required output power are analyzed and discussed in detail.
Predictive factors and treatment outcomes of Steinstrasse following shock wave lithotripsy for ureteral calculi: A Bayesian regression model analysis (2018)

Steinstrasse formation following SWL for ureter stone was rare event but nonnegligible. Large stone size, high stone attenuation and short SSD were significant predictors of Steinstrasse formation following SWL for ureter stone. Majority of patients with Steinstrasse formation could be treated conservatively in this clinical scenario.
[Human collagen IV lenses and epikeratoplasy in monkeys. Study of epithelial cicatrization]. (1991)

A previous study showed the good tolerance of the human type IV collagen lenses implanted by epikeratoplasty in 8 monkeys. It also showed type IV collagen is a good material for the reepithelialization. But we have been interested in the stability of the epithelial healing. The ultrastructural study found anchoring structures. However these were inconstant. So the authors try to understand better the mechanisms of this synthesis of the anchoring structures and describe the future ways of this experimental study.
Effect of Cyano Substitution on Non‐Fullerene Acceptor for Near‐Infrared Organic Photodetectors above 1000 nm (2022)

Abstract Near‐infrared organic photodetectors (NIR OPDs) comprising ultra‐narrow bandgap non‐fullerene acceptors (NFA, over 1000 nm) typically exhibit high dark current density under applied reverse bias. Therefore, suppression of dark current density is crucial to achieve high‐performance of such NIR OPDs. Herein, cyano (CN) with a strong electron‐withdrawing property is introduced into alkoxy thiophene as a π‐bridge to adjust its optoelectronic characteristics, and the correlation between dark current density and charge injection barrier is investigated. Compared with their motivated NFA (COTH), the novel CN‐substituted NFAs, COTCN and COTCN2, exhibited deeper‐lying highest occupied molecular orbital energy levels and narrower optical bandgap (&lt;1.10 eV), owing to the strong inductive and resonance effect of CN. The dark current and total noise currents are minimized as the number of substituted CN increases because of the larger hole injection barrier. Consequently, PTB7‐Th:COTCN2 exhibited the best shot‐noise limited detectivity ( D * sh , 1.18 × 10 12 Jones) and total noise detectivity ( D * n , 1.33 × 10 11 Jones) compared with those of PTB7‐Th:COTH ( D * sh , 2.47 × 10 11 Jones and D * n , 1.96 × 10 10 Jones).
Parallelization and performance analysis of reversible circuit synthesis (2018)

Rising popularity of quantum computers in the last decade resulted in increased interest paid to reversible circuit synthesis process. In this work, a popular essential function-based synthesis algorithm known in the literature is parallelized using openMP library. Contrary to conventional way, essential functions are synthesized when needed without keeping a table-lookup library. When the reversible circuit is synthesized in parallel using a double core processor (4 active threads with hyperthearding technology), around 2.6 speed-up is demonstrated relative to the performance of serial synthesis work. Comparison between serial and parallel synthesis by using common benchmark circuits demonstrated that the performance of the proposed parallel synthesis is always better in the overall operation work load.
HIV-1 neutralizing antibodies elicited by the candidate CBD1 epitope vaccine react with the conserved caveolin-1 binding motif of viral glycoprotein gp41 (2006)

To date, candidate HIV-1 vaccines that have been tested in clinical trials have failed to induce broadly neutralizing activities and/or antibodies that inhibit infection by primary isolates of HIV-1. We recently identified a conserved caveolin-1 binding motif, WNNMTWMQW, in the ectodomain of HIV-1 transmembrane envelope glycoprotein gp41. We designed the synthetic CBD1 peptide SLEQIWNNMTWMQWDK, corresponding to the consensus caveolin-1 binding domain (CBD) in gp41, and showed that it elicits in rabbits the production of antibodies that inhibit infection of primary CD4(+) T lymphocytes by various primary HIV-1 isolates. Although a conserved and highly homologous caveolin-1 binding motif is present in the transmembrane envelope glycoprotein of different HIV-2 isolates, anti-CBD1 immune sera do not inhibit HIV-2 infection. Here we show that anti-CBD1 antibodies are directed against the conserved caveolin-1 binding motif WNNMTWMQW in the CBD1 epitope. In spite of this, anti-CBD1 antibodies do not react with the CBD2 peptide SLTPDWNNMTWQEWER, corresponding to the potential consensus caveolin-1 binding domain in HIV-2. The presence of a conserved proline residue upstream of the caveolin-1 binding motif in CBD2 might affect the presentation of this motif, and thus account for the lack of reactivity of the immune sera. Anti-CBD1 antibodies therefore appear to be directed against a conformational epitope mimicked by the synthetic CBD1 peptide. In accordance with this, anti-CBD1 immune sera react with the native but not denatured gp41. The reactivity of anti-CBD1 immune sera with a highly conserved conformational epitope could explain the broad inhibitory activity of such antipeptide antibodies against HIV-1 isolates of various clades.
Mobile robot navigation with reactive free space estimation (2010)

One of the fundamental requirements of an autonomous mobile robot is that it must not collide with obstacles. This paper addresses the problem of controlling an autonomous robot to avoid obstacles for reactive route following navigation. The four-wheeled mobile robot is equipped with three monocular cameras for route following and a range sensor for obstacle avoidance. The equipped robot moves route environments using a reactive navigation method. When an obstacle is detected by a range sensor, the proposed obstacle avoidance method estimates the free space in the route and generates the turning direction vector for heading the robot to the free space which is wider than other space. We executed experiments about the navigation algorithm of the robot with an obstacle including curved path environments in this paper. Through the experiment results in various cases, it is discovered that the proposed method has a better time performance for obstacle avoidance in comparison with other conventional technique.
Platelet and osteoclast β 3 integrins are critical for bone metastasis (2003)

Mice with a targeted deletion of beta3 integrin were used to examine the process by which tumor cells metastasize and destroy bone. Injection of B16 melanoma cells into the left cardiac ventricle resulted in osteolytic bone metastasis in 74% of beta3+/+ mice by 14 days. In contrast, only 4% of beta3-/- mice developed bone lesions. Direct intratibial inoculation of tumor resulted in marrow replacement by tumor in beta3-/- mice, but no associated trabecular bone resorption as seen inbeta3+/+ mice. Bone marrow transplantation studies showed that susceptibility to bone metastasis was conferred by a bone marrow-derived cell. To dissect the roles of osteoclast and platelet beta3 integrins in this model of bone metastasis, osteoclast-defective src-/- mice were used. Src-null mice were protected from tumor-associated bone destruction but were not protected from tumor cell metastasis to bone. In contrast, a highly specific platelet aggregation inhibitor of activated alphaIIbbeta3 prevented B16 metastases. These data demonstrate a critical role for platelet alphaIIbbeta3 in tumor entry into bone and suggest a mechanism by which antiplatelet therapy may be beneficial in preventing the metastasis of solid tumors.
Generation of infinitely long phase screens for modeling of optical wave propagation in atmospheric turbulence (2008)

Numerical modeling of optical wave propagation in atmospheric turbulence is traditionally performed by using the so-called ‘split’-operator method, where the influence of the propagation medium's refractive index inhomogeneities is accounted for only within a set of infinitely narrow phase distorting layers (phase screens). These phase screens are generated on a numerical grid of finite size, which corresponds to a rather narrow slice (spatial area) of atmospheric turbulence. In several important applications including laser target tracking, remote sensing, adaptive optics, and atmospheric imaging, optical system performance depends on atmospheric turbulence within an extended area that significantly exceeds the area associated with the numerical grid. In this paper we discuss methods that allow the generation of a family of long (including infinitely long) phase screens representing an extended (in one direction) area of atmospheric turbulence-induced phase distortions. This technique also allows the generation of long phase screens with spatially inhomogeneous statistical characteristics.
Optical Mice (2011)

Optische Mäuse sind Hilfsmittel, um sich auf einem Bildschirm zu bewegen und sich durch die gewünschten Inhalte zu navigieren. Ein solches System kann entweder in eine herkömmliche Maus eingebaut werden, die man mit der Hand über eine Oberfläche schiebt (erster Teil dieses Kapitels), oder auch direkt am Bildschirm integriert sein, wie z. B. in einem Mobiltelefon, und man fährt nur noch mit dem Finger darüber (zweiter Teil dieses Kapitels).
Radiographic and Clinical Classification of Acquired Midtarsus Deformities (1998)

To develop a classification of midtarsus deformities, clinical examination and weightbearing radiographs were used to evaluate 131 feet in 109 patients (average age, 59+/-11 years) with those deformities. Patients were classified into four types based on anatomic location of the maximum deformity. Type I (N=43) showed deformity at the metatarsocuneiform joints medially and the fourth and fifth metatarsocuboid joints laterally, with plantarmedial and/or medial prominence. Type II (N= 60) had deformity at the naviculocuneiform joint medially and the fourth and fifth metatarsocuboid joints laterally; plantarlateral prominence was characteristic, although one-third had isolated or additional medial prominences. Type III (N=17) had major deformity in the perinavicular region, with a prominence plantarcentrally or plantarlaterally. Type IV (N=11) had deformity at the transverse tarsal joints with variable prominences. Each type was further subdivided into stages A, B, and C based on the severity of the deformity. In stage B, the midtarsus was coplanar with the metatarsocalcaneal plane. In stage A, the midtarsus was above this plane. In stage C, the midtarsus was below this plane. We concluded that midtarsus deformities can be classified as one of four types and one of three stages. Additional study is warranted to correlate this system with prognosis and treatment for this pathologic process.
Progress with the uncooled electroabsorption modulator integrated DFB laser (2008)

We have developed the uncooled electroabsorption modulator integrated distributed feedback (EA/DFB) lasers for small-footprint and low-power-consumption transceiver modulus. In this study, we used the temperature-tolerant InGaAlAs materials in EA modulator. We investigated the 10.7-Gbps, 40-km transmission performances over wide temperature range. The dynamic extinction ratio was 9.9 dB and 13.3 dB at the 10oC and 85oC. The modulated output power was more than +3.7 dBm even at 85oC. The long-term reliability was also investigated under APC condition at ambient temperature of 85oC with starting current of 120 mA. There was no significant degradation of the operation current up to 5000 hours. Uncooled 1300-nm range 25-Gbps and 43-Gbps EA/DFB lasers were also investigated. These devices will provide cost-effective 100-Gbps and 40-Gbps transceiver for next-generation high speed network system. A wide temperature ranged 12-km transmission with over 9.6-dB dynamic extinction ratio was demonstrated under 25-Gbps modulation. A 43-Gbps 10-km transmission was also demonstrated. The laser achieved clearly opened eye diagrams with dynamic extinction ratio of over 7-dB from 25oC to 85oC.
Plasma Carboxy-Terminal Provasopressin (Copeptin): A Novel Marker of Insulin Resistance and Metabolic Syndrome (2009)

Our findings indicate a novel cross-sectional association between plasma copeptin and measures of insulin resistance and MetSyn.
Data from Chimeric Antigen Receptors Directed at Mutant KRAS Exhibit an Inverse Relationship Between Functional Potency and Neoantigen Selectivity (2023)

&lt;div&gt;&lt;p&gt;Neoantigens are among the most intriguing potential immuno-oncology targets because, unlike many cancer targets that are expressed on normal tissues, they are by definition restricted to cancer cells. Medicines directed at common neoantigens such as mutant KRAS are especially interesting because they may offer the convenience and cost of an off-the-shelf therapy. However, all common KRAS mutations produce proteins that differ from the wild type at a single amino acid, creating challenges for molecular discrimination. We have undertaken an effort to optimize single-chain variable fragments (scFv) against peptide/major histocompatibility antigen complexes composed of HLA-A*11 and either G12V- or G12D-mutant KRAS peptides. These scFvs could in principle be used in chimeric antigen receptor (CAR) T-cell therapies for selected patients whose tumors bear either of these mutations. Here we show that optimization of such CARs involves a trade-off between potency and selectivity. We further show that targeting this family without high selectivity engenders risks of cross-reactivity against other members of the G-protein family to which KRAS belongs.&lt;/p&gt;Significance:&lt;p&gt;We report an effort to generate high potency, selective CARs directed at mutant KRAS peptides. Although the heavily optimized CARs maintain high selectivity against wild-type KRAS, they lose selectivity against other KRAS-related peptides derived from human proteins. To our knowledge, this work is the first to examine the trade-off between potency and selectivity with regard to KRAS pMHC-directed CARs, illustrating the challenge to achieve both sufficient potency and high selectivity.&lt;/p&gt;&lt;/div&gt;
Scalable and Resilient SARS-CoV-2 testing in an Academic Centre (2020)

Abstract The emergence of the novel coronavirus SARS-CoV-2 has led to a pandemic infecting more than two million people worldwide in less than four months, posing a major threat to healthcare systems. This is compounded by the shortage of available tests causing numerous healthcare workers to unnecessarily self-isolate. We provide a roadmap instructing how a research institute can be repurposed in the midst of this crisis, in collaboration with partner hospitals and an established diagnostic laboratory, harnessing existing expertise in virus handling, robotics, PCR, and data science to derive a rapid, high throughput diagnostic testing pipeline for detecting SARS-CoV-2 in patients with suspected COVID-19. The pipeline is used to detect SARS-CoV-2 from combined nose-throat swabs and endotracheal secretions/ bronchoalveolar lavage fluid. Notably, it relies on a series of in-house buffers for virus inactivation and the extraction of viral RNA, thereby reducing the dependency on commercial suppliers at times of global shortage. We use a commercial RT-PCR assay, from BGI, and results are reported with a bespoke online web application that integrates with the healthcare digital system. This strategy facilitates the remote reporting of thousands of samples a day with a turnaround time of under 24 hours, universally applicable to laboratories worldwide.