gebhart/patrepeval huggingface dataset:
The Neutrophil to Lymphocyte Ratio Is Associated With the Risk of Subsequent Dementia in the Framingham Heart Study (2021)

<b>Objective:</b> Active neutrophils are important contributors to Alzheimer's disease (AD) pathology through the formation of capillary stalls that compromise cerebral blood flow (CBF) and through aberrant neutrophil signaling that advances disease progression. The neutrophil to lymphocyte ratio (NLR) is a proxy of neutrophil-mediated inflammation, and higher NLR is found in persons diagnosed with clinical AD. The objective of this study was to investigate whether increased NLR in older adults is independently associated with the risk of subsequent dementia. <b>Methods:</b> We examined associations of baseline NLR with incident dementia risk in the community-based Framingham Heart Study (FHS) longitudinal cohorts. The association between NLR and risk of dementia was evaluated using the cumulative incidence function (CIF) and inverse probability-weighted Cox proportional cause-specific hazards regression models, with adjustment for age, sex, body mass index (BMI), systolic and diastolic blood pressure, diabetes, current smoking status, low-density lipoprotein (LDH), high-density lipoprotein (LDL), total cholesterol, triglycerides, and history of cardiovascular disease (CVD). Random forest survival models were used to evaluate the relative predictive value of the model covariates on dementia risk. <b>Results:</b> The final study sample included 1,648 participants with FHS (average age, 69 years; 56% women). During follow-up (median, 5.9 years), we observed 51 cases of incident dementia, of which 41 were AD cases. Results from weighted models suggested that the NLR was independently associated with incident dementia, and it was preceded in predictive value only by age, history of CVD, and blood pressure at baseline. <b>Conclusion:</b> Our study shows that individuals with higher NLR are at a greater risk of subsequent dementia during a 5.9-year follow-up period. Further evaluating the role of neutrophil-mediated inflammation in AD progression may be warranted.
Deep learning‐based quantification of arbuscular mycorrhizal fungi in plant roots (2021)

Soil fungi establish mutualistic interactions with the roots of most vascular land plants. Arbuscular mycorrhizal (AM) fungi are among the most extensively characterised mycobionts to date. Current approaches to quantifying the extent of root colonisation and the abundance of hyphal structures in mutant roots rely on staining and human scoring involving simple yet repetitive tasks which are prone to variation between experimenters. We developed Automatic Mycorrhiza Finder (AMFinder) which allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks. AMFinder delivered high-confidence predictions on image datasets of roots of multiple plant hosts (Nicotiana benthamiana, Medicago truncatula, Lotus japonicus, Oryza sativa) and captured the altered colonisation in ram1-1, str, and smax1 mutants. A streamlined protocol for sample preparation and imaging allowed us to quantify mycobionts from the genera Rhizophagus, Claroideoglomus, Rhizoglomus and Funneliformis via flatbed scanning or digital microscopy, including dynamic increases in colonisation in whole root systems over time. AMFinder adapts to a wide array of experimental conditions. It enables accurate, reproducible analyses of plant root systems and will support better documentation of AM fungal colonisation analyses. AMFinder can be accessed at https://github.com/SchornacklabSLCU/amfinder.
Passive Immunization with Recombinant Antibody VLRB-PirAvp/PirBvp—Enriched Feeds against Vibrio parahaemolyticus Infection in Litopenaeus vannamei Shrimp (2021)

The causative agent of acute hepatopancreatic necrosis disease (AHPND) is the bacterium, <i>Vibrio parahaemolyticus</i>, which secretes toxins into the gastrointestinal tract of its host. <i>Vibrio parahaemolyticus</i> toxins A and B (PirA<sup>vp</sup>/PirB<sup>vp</sup>) have been implicated in the pathogenesis of this disease, and are, therefore, the focus of studies developing treatments for AHPND. We previously produced recombinant antibodies based on the hagfish variable lymphocyte receptor B (VLRB) capable of neutralizing some viruses, suggesting that this type of antibody may have a potential application for treatment of AHPND. Here, recombinant PirA<sup>vp</sup>/PirB<sup>vp</sup>, produced using a bacterial expression system, were used as antigens to screen a hagfish VLRB cDNA library to obtain PirA<sup>vp</sup>/PirB<sup>vp</sup>-specific antibodies. A cell line secreting these antibodies was established by screening and cloning the DNA extracted from hagfish B cells. Supernatants collected from cells secreting the PirA<sup>vp</sup>/PirB<sup>vp</sup> antibodies were collected and concentrated, and used to passively immunize shrimp to neutralize the toxins PirA<sup>vp</sup> or PirB<sup>vp</sup> associated with AHPND. Briefly, 10 μg of PirA<sup>vp</sup> and PirB<sup>vp</sup> antibodies, 7C12 and 9G10, respectively, were mixed with the shrimp feed, and fed to shrimp for three days consecutive days prior to experimentally infecting the shrimp with <i>V. parahaemolyticus</i> (containing toxins A and B), and resulting mortalities recorded for six days. Results showed significantly higher level of survival in shrimp fed with the PirB<sup>vp</sup>-9G10 antibody (60%) compared to the group fed the PirA<sup>vp</sup>-7C12 antibody (3%) and the control group (0%). This suggests that VLRB antibodies may be a suitable alternative to immunoglobulin-based antibodies, as passive immunization treatments for effective management of AHPND outbreaks within shrimp farms.
Scalable Correct Memory Ordering via Relativistic Programming (2011)

We propose and document a new concurrent pro-gramming model, relativistic programming. This model allows readers to run concurrently with writ-ers, without blocking or using expensive synchro-nization. Relativistic programming builds on exist-ing synchronization primitives that allow writers to wait for current readers to finish with minimal reader overhead. Our methodology models data structures as graphs, and reader algorithms as traversals of these graphs; from this foundation we show how writers can implement arbitrarily strong ordering guarantees for the visibility of their writes, up to and including total ordering. 1
Packaging and Thermal Decoupling of an Optical Array using a Thermoelectric Cooler (2018)

Today's compact electronic packages consist of chips with different restrictions on their operating temperatures. To ensure reliability in such devices, each component must be kept within their temperature limits. This often results in overcooling the entire package to meet the lowest temperature limit that exists within the system, leading to an inefficient thermal management scheme. By implementing localized cooling, the chips with lower operating temperatures can be thermally de-coupled from the rest of the package, providing a more energy efficient solution. Thermoelectric coolers are favorable candidates for such localized cooling, due to their compact form-factor and solid-state nature. Thus, in this paper, the utilization of a thermoelectric cooler to thermally de-couple an optical array-with a temperature limitation of 85°C-from a larger electronic device-with a temperature limitation of 105°C-is investigated. The system is initially modeled in the commercially available FEM software ANSYS for illustrating the theoretical enhancement of using a thermoelectric cooler. Finally, a test setup of the actual stack-up is built and the thermal de-coupling is experimentally demonstrated using a commercially available thermoelectric cooler.
Deconvolution of narrow boron SIMS depth profiles in Si and SiGe (1995)

Abstract We present results on deconvolution of molecular beam epitaxy (MBE)‐grown boron profiles in Si and SiGe that are of crucial importance for Si/SiGe heterojunction bipolar transistors (HBTs). They are based on the assumptions of linearity and homogeneity of the measurement. We determine experimentally the physical limits of these assumptions by investigating sequences of boron spikes in Si and SiGe. The deconvolution is performed by Fourier transformation into the k ‐domain, preceded by a physically motivated least‐squares fitting of the measurement data. In this way, the high‐frequency noise contributions are eliminated to a great extent without producing a systematic broadening. The numerical evaluation of the SIMS profiles is extremely fast in comparison to forward techniques and the numerical error is shown to be small. We discuss the deconvoluted SIMS profiles of MBE‐grown boron spikes in Si and SiGe after annealing. Our method is suited to give information about the dopant outdiffusion from th SiGe layer in the case of HBTs.
One-Pot Synthesis of 5-(Ethoxymethyl)furfural from Glucose Using Sn-BEA and Amberlyst Catalysts (2012)

5-(Ethoxymethyl)furfural (EMF) was produced from glucose in ethanol in a single reactor at 90 °C. The reaction proceeds via the isomerization of glucose to fructose with zeolite Sn-Beta, a Lewis acid catalyst. Fructose is converted to 5-(hydroxymethyl)furfural, which is then etherified to EMF using a Brønsted acid catalyst, Amberlyst 131. An EMF yield of 31% was achieved.
New developments in tissue-type imaging (TTI) of prostate cancer: combined ultrasonic and magnetic-resonance methods (2006)

Because current methods of imaging prostate cancer are inadequate, biopsies cannot be guided effectively and treatment cannot be planned, targeted or monitored optimally. Therefore, our research is aimed at ultrasonically characterizing cancerous prostate tissue so that we can image it more effectively and thereby provide improved means of detecting, treating, and monitoring prostate cancer. We base our characterization methods on spectrum analysis of radiofrequency (RF) ultrasonic (US) echo signals combined with clinical variables such as prostate-specific antigen (PSA). We classify parameters of US spectra (USS) using artificial neural networks (ANNs), and express classification efficacy using relative-operating- characteristic (ROC) methods. The US methods produce ROC- curve areas of 0.84 compared to 0.64 for conventional methods. We generate lookup tables (LUTs) that translate spectral parameters and clinical variables directly to pixel values in tissue-type images (TTIs) that show cancerous regions in 2- or 3- D. Based on encouraging results obtained by others using magnetic-resonance spectroscopy (MRS) for identifying cancerous prostate lesions, we are investigating means of combining MRS with USS methods to produce multimodality TTIs.
Day-Surgery Patients Anesthetized with Propofol Have Less Postoperative Pain than Those Anesthetized with Sevoflurane (2010)

The patients anesthetized with propofol appeared to have less pain than patients anesthetized with sevoflurane.
<title>Tomographic processing on wireless ground sensor networks</title> (2001)

New opportunities for battlefield surveillance and modeling are unfolding with the advent of smart sensors linked via digital wireless networks. One exciting prospect is the use of tomographic techniques in order to create real-time three-dimensional modeling and analysis of the environment that is immediately accessible to battlefield forces. We have developed a small-scale ground sensor network for this application. We discuss initial deployment of this network as a tracking system.
Lookout for Zombies: Mitigating Flush+Reload Attack on Shared Caches by\n Monitoring Invalidated Lines (2019)

OS-based page sharing is a commonly used optimization in modern systems to\nreduce memory footprint. Unfortunately, such sharing can cause Flush+Reload\ncache attacks, whereby a spy periodically flushes a cache line of shared data\n(using the clflush instruction) and reloads it to infer the access patterns of\na victim application. Current proposals to mitigate Flush+Reload attacks are\nimpractical as they either disable page sharing, or require application\nrewrite, or require OS support, or incur ISA changes. Ideally, we want to\ntolerate attacks without requiring any OS or ISA support and while incurring\nnegligible performance and storage overheads.\n This paper makes the key observation that when a cache line is invalidated\ndue to a Flush-Caused Invalidation (FCI), the tag and data of the invalidated\nline are still resident in the cache and can be used for detecting Flush-based\nattacks. We call lines invalidated due to FCI as Zombie lines. Our design\nexplicitly marks such lines as Zombies, preserves the Zombie lines in the\ncache, and uses the hits and misses to Zombie lines to tolerate the attacks. We\npropose Zombie-Based Mitigation (ZBM), a simple hardware-based design that\nsuccessfully guards against attacks by simply treating hits on Zombie-lines as\nmisses to avoid any timing leaks to the attacker. We analyze the robustness of\nZBM using three spy programs: attacking AES T-Tables, attacking RSA\nSquare-and-Multiply, and Function Watcher (FW), and show that ZBM successfully\ndefends against these attacks. Our solution requires negligible storage (4-bits\nper cache line), retains OS-based page sharing, requires no OS/ISA changes, and\ndoes not incur slowdown for benign applications.\n
Midodrine prevents orthostatic intolerance associated with simulated spaceflight (2001)

Many astronauts after being weightless in space become hypotensive and presyncopal when they assume an upright position. This phenomenon, known as orthostatic intolerance, may interfere with astronaut function during reentry and after spaceflight and may limit the ability of an astronaut to exit a landed spacecraft unaided during an emergency. Orthostatic intolerance is more pronounced after long-term spaceflight and is a major concern with respect to the extended flights expected aboard the International Space Station and for interplanetary exploration class missions, such as a human mission to Mars. Fully effective countermeasures to this problem have not yet been developed. To test the hypothesis that alpha-adrenergic stimulation might provide an effective countermeasure, we conducted a 16-day head-down-tilt bed-rest study (an analog of weightlessness) using normal human volunteers and administered the alpha(1)-agonist drug midodrine at the end of the bed-rest period. Midodrine was found to significantly ameliorate excessive decreases in blood pressure and presyncope during a provocative tilt test. We conclude that midodrine may be an effective countermeasure for the prevention of orthostatic intolerance following spaceflight.
In Scan Room No-Interference High Efficiency Switching Power Supply with GaN (2023)

A switching regulator implemented with GaN power semiconductors and air core inductors was shown not to create any noise that affected the scanner imaging. This was due to the selected switching frequency of 2.489MHz, which avoided harmonics at imaging frequencies of interest. The switching regulator size and thermal management at 90% does not require any additional support systems in the scan room. This demonstrates that GaN-based switching regulators can be a good solution to regulate voltages in the scan room and also significantly reduce the cabling and simplify installation.
Denial of service flaws in SDI software-an initial assessment (2003)

The author provides a tutorial and survey into the denial-of-service aspect of computer security. Definitions from existing literature are presented, and several categorizations of potential denial-of-service flaws are provided with examples from actual cases. Methods for providing preventive resistance against denial-of-service threats as well as mechanisms for detection and recovery from denial-of-service flaws are presented. The application of these methods and mechanisms with respect to software developed for the Strategic Defense Initiative (SDI), program is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Erbium Nanoparticle Doping for Power Scaling of Fiber Lasers (2016)

Nanoparticle doping was used for making erbium-doped fibers. We report luminescence lifetimes greater than for solution doped fibers, high optical-to-optical slope efficiencies and an increase in the stimulated Brillouin scattering threshold.
Epstein–Barr virus: Induction and control of cell transformation (2003)

Epstein-Barr virus (EBV), a ubiquitous human herpes virus, is associated with an increasing number of lymphoid and epithelial malignancies. The ability of the virus to establish life-long persistent infections and induce growth transformation is related to the function of a set of viral proteins that are variously expressed in both normal and malignant cells. Recent evidence indicates that these viral proteins are able to usurp cellular pathways that promote the cell growth and survival, while impairing anti-viral immune responses. Elucidation of the mechanisms by which EBV induces cell transformation and escapes host immune control provides the rational background for the design of new strategies of intervention for EBV-related malignancies.
Measuring electrical conductivity at low frequency using the eddy currents induced by the imaging gradients (2012)

To measure the complex permittivity or only the conductivity non-invasively, several methods were proposed. In MR current density imaging (MR-CDI), an external current source is connected to the skin to inject current into the tissue. Using some post-processing steps, theconductivity can be derived from the obtained current density map,this is called MR electrical impedance mapping (MR-EIT). MR-CDI andMR-EIT is generally performed using a DC current for a few ms, i.e.,the obtained complex permittivity belongs to the low frequency range (below ~1kHz). Recently, a new method was developed, for which no external source was needed anymore. Using this method, the complexpermittivity is measured at the Larmor frequency. Both MR-CDI and MR-EIT require an external current source, which is not present on astandard MR machine. This current source should be connected to theskin to inject a current. A major concern of these methods is the high current needed to obtain sufficient SNR, and the consequential pain induced in the subject. For MR-EPT (in the following called RF-EPT), no additional equipment is needed besides an MR scanner, and no current is injected. However, the applied frequency is limited tothe Larmor frequency of the MR scanner. The newly proposed method, called gradient-EPT, uses the EM fields induced by the gradients applied for MR spatial encoding. This combines the advantages of bothMR-EIT/MR-CDI (frequency of particular biologic interest) and RF-EPT(no current injection). This study is based on the insight that thedistribution of eddy currents induced in the body by gradient switching depends on the local dielectric properties of tissue. During the ramping of the gradients, currents will be induced through the process of induction. The current will be affected by the local conductivity of the tissue. This induced current will locally alter the main magnetic field, to be measured using phase imaging.
Translational significance of Nodal, Cripto-1 and Notch4 in adult nevi (2016)

The TGF-β associated growth factor Nodal is highly expressed in aggressive metastatic melanoma. Determining the risk for melanomagenesis from Nodal expression in nevi prior to the development of melanoma may be useful for both the screening and prevention of melanoma. Tissue sections of human adult nevi with or without a history of melanoma were stained by immunohistochemistry (IHC) for Nodal, the Nodal co-receptor Cripto-1, and Notch4, which have previously been shown to be associated with Nodal expression in melanoma. The degree of Nodal, Cripto-1 and Notch4 staining was scored and correlated with available clinical data. Median IHC scores for Nodal, Cripto-1 and Notch4 expression were significantly higher in nevi removed from patients who eventually developed melanoma compared with nevi from patients with no history of melanoma. In addition, the degree of Nodal expression in nevi from patients who eventually developed melanoma correlated significantly with the Breslow depth of the melanoma. Expression of Nodal and components of its signaling pathway in nevi may represent a biomarker for selecting a unique subset of patients requiring increased surveillance for screening and prevention of melanoma.
Reduced-illuminance autofluorescence imaging in ABCA4-associated retinal degenerations (2007)

The health of the retinal pigment epithelium (RPE) can be estimated with autofluorescence (AF) imaging of lipofuscin, which accumulates as a byproduct of retinal exposure to light. Lipofuscin may be toxic to the RPE, and its toxicity may be enhanced by short-wavelength (SW) illumination. The high-intensity and SW excitation light used in conventional AF imaging could, at least in principle, increase the rate of lipofuscin accumulation and/or increase its toxicity. We considered two reduced-illuminance AF imaging (RAFI) methods as alternatives to conventional AF imaging. RAFI methods use either near-infrared (NIR) light or reduced-radiance SW illumination for excitation of fluorophores. We quantified the distribution of RAFI signals in relation to retinal structure and function in patients with the prototypical lipofuscin accumulation disease caused by mutations in ABCA4. There was evidence for two subclinical stages of macular ABCA4 disease involving hyperautofluorescence of both SW- and NIR-RAFI with and without associated loss of visual function. Use of RAFI methods and microperimetry in future clinical trials involving lipofuscinopathies should allow quantification of subclinical disease expression and progression without subjecting the diseased retina/RPE to undue light exposure.
T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable (2018)

HIV controllers (HCs) are individuals who can naturally control HIV infection, partially due to potent HIV-specific CD8+ T cell responses. Here, we examined the hypothesis that superior function of CD8+ T cells from HCs is encoded by their T cell receptors (TCRs). We compared the functional properties of immunodominant HIV-specific TCRs obtained from HLA-B*2705 HCs and chronic progressors (CPs) following expression in primary T cells. T cells transduced with TCRs from HCs and CPs showed equivalent induction of epitope-specific cytotoxicity, cytokine secretion, and antigen-binding properties. Transduced T cells comparably, albeit modestly, also suppressed HIV infection in vitro and in humanized mice. We also performed extensive molecular dynamics simulations that provided a structural basis for similarities in cytotoxicity and epitope cross-reactivity. These results demonstrate that the differential abilities of HIV-specific CD8+ T cells from HCs and CPs are not genetically encoded in the TCRs alone and must depend on additional factors.
ChemInform Abstract: A FUNCTIONALIZED TRISECODODECAHEDRANE HAVING C2 SYMMETRY (1977)

Abstract Aus der Dicarbonsäure (I) wird durch Jodlactonisierung, basenkatalysierte Methanolyse des Bis‐[jodlactons], Jones‐Oxidation und reduktive Dejodierung des Methanolyseprodukts der Diketodicarbonsäureester (II) dargestellt.