gebhart/patrepeval huggingface dataset:
Fatal Mycotic Aneurysm of the Basilar Artery Caused by Aspergillus fumigatus in a Patient with Pituitary Adenoma and Meningitis (2017)

Fungal infections of the central nervous system (CNS) frequently occur in immunosuppressed patients. Here, we describe the case of an immunocompetent 64-year-old man who presented with diplopia, right-sided hemiparesis, and a mild headache after cleaning and replacing nesting boxes of wild birds during the preceding months. Lumbar puncture revealed pleocytosis, elevated protein, and lactate levels in the cerebrospinal fluid (CSF). Initial imaging showed ischemia in the left thalamus and an enlargement of the sellar region. Antibiotic treatment and corticosteroids led to an initial improvement but was followed by rapid deterioration. Antibiotic treatment was modified and antifungal therapy was added. Eighteen days after admission, the patient died from a subarachnoid hemorrhage resulting from the rupture of a fusiform aneurysm of the basilar artery. Microbiological culture of CSF was negative, but a positive galactomannan assay suggested fungal infection which was corroborated by detection of <i>Aspergillus fumigatus</i> DNA in pan-fungal PCR and sequencing. The presence of septated hyphae in the wall of the basilar artery confirmed the diagnosis of a mycotic aneurysm caused by hyphomycetal infection. In addition, brain autopsy revealed the presence of an invasive adrenocorticotrophic hormone-producing pituitary adenoma with arrosion of the sellar bone. This process and its invasiveness likely facilitated the spread of the fungal pathogen from the sphenoid sinus to the dura mater and finally led to cerebral angioinvasion. Our case demonstrates the challenge to timely diagnose and effectively treat aspergillosis as a cause of CNS infection also in apparently immunocompetent patients. The potential of assays detecting fungal antigens and of PCR to facilitate a timely diagnosis is discussed.
Train and deploy a community level public health workforce to combat covid-19 (2020)

We strongly support Pollock and colleagues’ views.1 We do not understand why the government did not follow World Health Organization guidelines regarding basic infection control practice2 on contact tracing in the early days of the pandemic. We welcome the plan to train 18 000 contact tracers but, in the government’s current proposal, the public are in danger of being seen as …
Urine Analysis and Protein Networking Identify Met as a Marker of Metastatic Prostate Cancer (2009)

Urinary met may provide a noninvasive biomarker indicative of metastatic prostate cancer and may be a central regulator of multiple pathways involved in prostate cancer progression.
Modeling of photon migration in the human lung using a finite volume solver (2006)

The application of the frequency domain and steady-state diffusive optical spectroscopy (DOS) and steady-state near infrared spectroscopy (NIRS) to diagnosis of the human lung injury challenges many elements of these techniques. These include the DOS/NIRS instrument performance and accurate models of light transport in heterogeneous thorax tissue. The thorax tissue not only consists of different media (e.g. chest wall with ribs, lungs) but its optical properties also vary with time due to respiration and changes in thorax geometry with contusion (e.g. pneumothorax or hemothorax). This paper presents a finite volume solver developed to model photon migration in the diffusion approximation in heterogeneous complex 3D tissues. The code applies boundary conditions that account for Fresnel reflections. We propose an effective diffusion coefficient for the void volumes (pneumothorax) based on the assumption of the Lambertian diffusion of photons entering the pleural cavity and accounting for the local pleural cavity thickness. The code has been validated using the MCML Monte Carlo code as a benchmark. The code environment enables a semi-automatic preparation of 3D computational geometry from medical images and its rapid automatic meshing. We present the application of the code to analysis/optimization of the hybrid DOS/NIRS/ultrasound technique in which ultrasound provides data on the localization of thorax tissue boundaries. The code effectiveness (3D complex case computation takes 1 second) enables its use to quantitatively relate detected light signal to absorption and reduced scattering coefficients that are indicators of the pulmonary physiologic state (hemoglobin concentration and oxygenation).
Data from Tumor Immunogenomic Features Determine Outcomes in Patients with Metastatic Colorectal Cancer Treated with Standard-of-Care Combinations of Bevacizumab and Cetuximab (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;CALGB/SWOG 80405 was a randomized phase III trial in first-line patients with metastatic colorectal cancer treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on overall survival (OS).&lt;/p&gt;Experimental Design:&lt;p&gt;Primary tumors (&lt;i&gt;N&lt;/i&gt; = 554) were profiled by RNA sequencing. Immune signatures of macrophages, lymphocytes, TGFβ, IFNγ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8&lt;sup&gt;+&lt;/sup&gt; T cells, resting and activated memory CD4&lt;sup&gt;+&lt;/sup&gt; T cells, M0 and M2 macrophages, and activated mast cells were measured.&lt;/p&gt;Results:&lt;p&gt;Increased M2 macrophage score [HR, 6.30; 95% confidence interval (CI), 3.0–12.15] and TGFβ signature expression (HR, 1.35; 95% CI, 1.05–1.77) were associated with shorter OS. Increased scores of plasma cells (HR, 0.55; 95% CI, 0.38–0.87) and activated memory CD4&lt;sup&gt;+&lt;/sup&gt; T cells (HR, 0.34; 95% CI, 0.16–0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0–1 beneficial features associated with longer OS, and the median (95% CI) OS decreased from 42.5 (35.8–47.8) to 31.0 (28.8–34.4), 25.2 (20.6–27.9), and 17.7 (13.5–20.4) months respectively (&lt;i&gt;P&lt;/i&gt; = 3.48e–11).&lt;/p&gt;Conclusions:&lt;p&gt;New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.&lt;/p&gt;&lt;/div&gt;
Anisotropic Etching of Silicon (1969)

A ternary liquid etchant solution for silicon, consisting of hydrazine, iso-2-propyl alcohol (IPA), and water has been studied in some detail. In common with other anisotropic etchants reported in the literature, marked dependence of dissolution rate on the crystal orientation of the etched surface has been observed with a low rate of attack on (111) planes. In contrast to other formulations, this etch attacks neither silicon dioxide nor aluminium vacuum-deposited films, either of which may be used as a very convenient in-contact masking medium for the engraving of intricate shapes on an appropriately oriented silicon substrate. The experimental study indicates that the etch velocity is a maximum for (211) planes, which accounts for the rounding of convex corners frequently observed when engraving regular shapes in silicon with anisotropic etches. The optimum etch solution is an equimolar mixture of NH2 and H2O.
Fuzzy-logic digital-analogue interfaces for accurate mixed-signal simulation (1998)

A new approach to mixed-signal circuit interfacing based on fuzzy logic models is presented. Due to their continuous rather than discrete character fuzzy logic models offer a significant improvement compared with the classical D-A interface models. Fuzzy logic D-A interfaces can represent the boundary between the digital and analogue worlds accurately without a significant loss of computational efficiency. The potential of mixed-signal signal interfacing based on fuzzy logic is demonstrated by an example of spike propagation from the digital to analogue world. A model of inertial propagation delay and non-linear DC gain suitable for fuzzy logic gates is also suggested.
Perceptual weighting deep neural networks for single-channel speech enhancement (2016)

Improving the perceptual quality of speech signals is a key yet challenging problem for many real world applications. In this paper, we propose a perceptually motivated approach based on deep neural networks (DNNs) for speech enhancement task. The proposed approach take into consider the masking properties of the human auditory system and reduces the perceptual effect of the residual noise. Given the good performance of deep learning in signal representation, a DNN is employed for accurately modeling the clean speech spectrum. In the DNN training stage, perceptual weighting matrix is used to adjust the weight of the error when using back propagation algorithm transfer the error from DNN output layer to the front layer. Evaluations on various real-world background noises show that the proposed method performs better than different competitive methods.
Helicobacter pylori Eradication in Drug-related Peptic Ulcer (2020)

Non-steroidal anti-inflammatory drugs (NSAIDs) and aspirin are the most frequently prescribed drugs worldwide, and their long-term use often leads to peptic ulcers (PUs) along with serious complications, such as bleeding and perforation. <i>Helicobacter pylori</i> (<i>H. pylori</i>) infection is a significant risk factor for developing NSAID-related PU and ulcer bleeding during long-term aspirin use. In a revised version of the Clinical Guidelines for Drug-induced Peptic Ulcer, two statements regarding <i>H. pylori</i> eradication are recommended. 1) Patients scheduled for long-term NSAID therapy should be tested and treated for <i>H. pylori</i> infection to prevent PU and its complications. 2) Patients with a history of PU receiving long-term low-dose aspirin (LDA) therapy should undergo treatment for <i>H. pylori</i> infection to prevent PU and its complications. On the other hand, unlike NSAID-naïve patients, the preventive effects of <i>H. pylori</i> eradication in chronic NSAID users are unclear. In addition, anti-ulcer drugs, such as proton pump inhibitors, may be necessary for maintenance therapy after <i>H. pylori</i> eradication in a subset of long-term LDA users, particularly if the patients are taking concomitant antiplatelet agents or anticoagulants.
Potential automata. Application to the genetic code III (2006)

In previous notes, we have described both mathematical properties of potential (n-switches) and potential-Hamiltonian (Liénard systems) continuous differential systems, and also biological applications, especially those concerning primitive cyclic RNAs related to the genetic code. In the present note, we give a general definition of a potential automaton, and we show that a discrete Hopfield-like system already introduced by Goles et al. is a good candidate for such a potential automaton: it has a Lyapunov functional that decreases on its trajectories and whose time derivative is just its discrete velocity. Then we apply this new notion of potential automaton to the genetic code. We show in particular that the consideration of only physicochemical properties of amino-acids, like their molecular weight, hydrophobicity and ability to create hydrogen bonds suffices to build a potential decreasing on trajectories corresponding to the synonymy classes of the genetic code. Such an 'a minima' construction reinforces the classical stereochemical hypothesis about the origin of the genetic code and authorizes new views about the optimality of its synonymy classes.
Peripheral peptide YY inhibits propulsive colonic motor function through Y2receptor in conscious mice (2009)

Peptide YY (PYY) antisecretory effect on intestinal epithelia is well established, whereas less is known about its actions to influence colonic motility in conscious animals. We characterized changes in basal function and stimulated colonic motor function induced by PYY-related peptides in conscious mice. PYY(3-36), PYY, and neuropeptide Y (NPY) (8 nmol/kg) injected intraperitoneally inhibited fecal pellet output (FPO) per hour during novel environment stress by 90%, 63%, and 57%, respectively, whereas the Y(1)-preferring agonists, [Pro(34)]PYY and [Leu(31),Pro(34)]NPY, had no effect. Corticotrophin-releasing factor 2 receptor antagonist did not alter PYY(3-36) inhibitory action. PYY and PYY(3-36) significantly reduced restraint-stimulated defecation, and PYY(3-36) inhibited high-amplitude distal colonic contractions in restrained conscious mice for 1 h, by intraluminal pressure with the use of a microtransducer. PYY suppression of intraperitoneal 5-hydroxytryptophan induced FPO and diarrhea was blocked by the Y(2) antagonist, BIIE0246, injected intraperitoneally and mimicked by PYY(3-36), but not [Leu(31),Pro(34)]NPY. PYY(3-36) also inhibited bethanechol-stimulated FPO and diarrhea. PYY(3-36) inhibited basal FPO during nocturnal feeding period and light phase in fasted/refed mice for 2-3 h, whereas the reduction of food intake lasted for only 1 h. PYY(3-36) delayed gastric emptying after fasting-refeeding by 48% and distal colonic transit time by 104%, whereas [Leu(31),Pro(34)]NPY had no effect. In the proximal and distal colon, higher Y(2) mRNA expression was detected in the mucosa than in muscle layers, and Y(2) immunoreactivity was located in nerve terminals around myenteric neurons. These data established that PYY/PYY(3-36) potently inhibits basal and stress/serotonin/cholinergic-stimulated propulsive colonic motor function in conscious mice, likely via Y(2) receptors.
Nanofocusing of light using three-dimensional plasmonic mode conversion (2013)

Efficient nanofocusing of light into a gap plasmon waveguide using three-dimensional mode conversion in a strip plasmonic directional coupler is proposed. Unlike conventional nanofocusing using tapering structures, a plasmonic directional coupler converts E(z)-type odd mode energy into E(y)-type gap plasmon mode by controlling phase mismatch and gap spacing. The simulation result shows the maximum electric field intensity increases up to 58.1 times the input intensity, and 17.3% of the light is focused on the nano gap region.
Constant-quality constrained-rate allocation for FGS video coded bitstreams (2002)

This paper proposes an optimal rate allocation scheme for Fine-Granular Scalability (FGS) coded bitstreams that can achieve constant quality reconstruction of frames under a dynamic rate budget constraint. In doing so, we also aim to minimize the overall distortion at the same time. To achieve this, we propose a novel R-D labeling scheme to characterize the R-D relationship of the source coding process. Specifically, sets of R-D points are extracted during the encoding process and linear interpolation is used to estimate the actual R-D curve of the enhancement layer signal. The extracted R-D information is then used by an enhancement layer transcoder to determine the bits that should be allocated per frame. A sliding window based rate allocation method is proposed to realize constant quality among frames. This scheme is first considered for a single FGS coded source, then extended to operate on multiple sources. With the proposed scheme, the rate allocation can be performed in a single pass, hence the complexity is quite low. Experimental results confirm the effectiveness of the proposed scheme under static and dynamic bandwidth conditions.
Effect of Li2O/Al Cathode in Alq3 Based Organic Light-Emitting Diodes (2008)

An effect of bilayer cathode Li20/Al was studied in Alq3 based organic light-emitting diodes with a variation of Li2O layer thickness. The current-luminance-voltage characteristics of ITO/TPD/Alq3/Li2O/Al device were measured at ambient condition to investigate the effect of Li2O/Al. It was found that when the thickness of Li2O layer is in the range of 0.5-1 nm, there are improvements in luminance, efficiency, and turn-on voltage of the device. A current density and a luminance are increased by about 100 times, a turn-on voltage is lowered from 6 V to 3 V, a maximum current efficiency is improved by a factor of 2.3, and a maximum power efficiency is improved by a factor of 3.2 for a device with a use of thin Li2O layer compared to those of the one without the Li2Otron-barrier height for electron injection from the cathode to the emissive layer.
Permanent-magnet machines with powdered iron cores and prepressed windings (2000)

This paper presents a permanent-magnet servomotor, built with a powdered iron stator, which has been designed to take full advantage of the properties of the material. There are a number of important design features which are not possible with laminated cores. For example, the core back is axially extended over the end windings, the armature core components are subdivided and preformed stator coils are used. The coils are prepressed to form a solid component with an exceptionally high fill factor (78%). The prototype offers far superior performance to a conventionally laminated commercial machine, manufactured in the same frame.
Particular etiology in a case of peripheral tetraparesis (2019)

Lead intoxication is a rare but potentially fatal disease without appropriate intervention. The diagnosis is often difficult because of various organs involvement. We report the case of nonprofessional lead intoxication manifested by tetraparesis, severe anemia, and hemolysis in a patient having also unknown beta thalassemia minor.
BIS and the Electromyogram (2006)

In Response: Drs. Renna and Gillbe are right (1) when they stated that they reported electromyographic (EMG) effects on bispectral index (BIS) during large-dose opioid induction (2). When compared with our methodology (3), theirs was more sophisticated: one group of 13 patients received 50 mcg/kg of fentanyl and a second group of 13 patients received 10 mcg/kg of fentanyl plus 0.2 mcg/kg of etomidate. They used a backward stepwise multiple regression analysis including five items to evaluate the relationship of BIS-EMG. Our simpler model mimics everyday practice: propofol titrated to loss of consciousness, followed by a bolus of atracurium (or placebo in the control group) 2 min after loss of consciousness. We demonstrated the BIS-myorelaxation relationship using simple statistical analysis. Nevertheless, our conclusions are in agreement with theirs. Ngai Liu, MD Thierry Chazot, MD Marc Fischler, MD Department of Anesthesiology Hôpital Foch [email protected]
The renin angiotensin system: importance in physiology and pathology (1989)

Angiotensin II has long been recognized as a key factor in cardiovascular regulation. The effectiveness of angiotensin-converting enzyme (ACE) inhibitors in controlling essential hypertension suggests that angiotensin II plays a key role in its pathology. The tools of molecular biology have provided the means for a critical reassessment of the renin-angiotensin-aldosterone system in physiology and pathology. The analysis has shown that angiotensin peptides are also synthesized and processed locally in a variety of tissues, including the vascular wall, adrenal glands, heart, and brain. Since angiotensin II is a potent modulator of cardiovascular control centers in the brain, the hypothesis is now advanced that a defect in the brain renin-angiotensin-aldosterone system contributes to the development of hypertensive disease.
The role of incretins in salt-sensitive hypertension (2011)

Incretin mimetics and DPP-IV inhibitors are a novel class of antihypertensive drugs with natriuretic properties. They can be used in the treatment of salt-sensitive hypertension, which is characterized by edema.
Drying Kinetics of Tomato Slices in Vacuum Assisted Solar and Open Sun Drying Methods (2007)

A lab model vacuum-assisted solar dryer was developed to study the drying kinetics of tomato slices (4, 6, and 8 mm thicknesses) compared with open sun drying under the weather conditions of Montreal, Canada. The drying study showed that the time taken for drying of tomato slices of 4, 6, and 8 mm thicknesses from the initial moisture content of 94.0% to the final moisture content of around 11.5 ± 0.5% (w.b.) was 360, 480, and 600 min in vacuum-assisted solar dryer and 450, 600, and 750 min in open sun drying, respectively. During drying, it was observed that the temperature inside the vacuum chamber was increased to 48°C when the maximum ambient temperature was only 30°C. The quality of tomato slices dried under vacuum-assisted solar dryer was of superior quality in terms of color retention and rehydration ratio. The drying kinetics using thin-layer drying models and the influence of weather parameters such as ambient air temperature, relative humidity, solar insolation, and wind velocity on drying of tomato slices were evaluated.
Plasma Amyloid-β (Aβ42) Correlates with Cerebrospinal Fluid Aβ42 in Alzheimer’s Disease (2018)

The 42 amino acid form of amyloid-β (Aβ42) plays a key role in the pathogenesis of Alzheimer's disease (AD) and is a core biomarker for the diagnosis of AD. Numerous studies have shown that cerebrospinal fluid (CSF) Aβ42 concentrations are decreased in AD, when measured by enzyme-linked immunosorbent assay (ELISA) and other conventional immunoassays. While most studies report no change in plasma Aβ42, independent studies using the immunomagnetic reduction (IMR) technique report an increase in plasma Aβ42 levels in AD. To confirm the opposite changes of Aβ42 levels in CSF and plasma for AD, we assayed the levels of Aβ42 in plasma of subjects with known CSF Aβ42 levels. In total 43 controls and 63 AD patients were selected at two sites: the VU University Medical Center (n = 55) and Sahlgrenska University Hospital (n = 51). IMR and ELISA were applied to assay Aβ42 in plasma and CSF, respectively. We found a moderately negative correlation between plasma and CSF Aβ42 levels in AD patients (r = -0.352), and a weakly positive correlation in controls (r = 0.186). These findings further corroborate that there are opposite changes of Aβ42 levels in CSF and plasma in AD. The possible causes for the negative correlation are discussed by taken assay technologies, Aβ42 transport from brain to peripheral blood, and sample matrix into account.
Principles for Human-Centered Interaction Design, Part 1: Performative Systems (2014)

This article discusses principles underlying the design of human-centered interfaces, using the specific example of the OZ cockpit display, which has no traditional dials or gauges.
Optimizing the use of gene expression data to predict metabolic pathway memberships (2020)

Expression matrix
Simulation of the Electric Field and Potential for a Micro Pattern X-ray Detector Using Maxwell Software (2021)

In the summer of 2007, the faculty and student team (FaST) program from Southern University in Baton Rouge, Louisiana supported by NSF, DOE, and LS-LAMP conducted a detailed study to design, simulate, build and test a micro-pattern x-ray fluorescence gas detector at Brookhaven National Laboratory (BNL). We used AutoCAD to design the detector's parts that were machined and assembled to form the proposed detector. We have used Maxwell software to predict the electrical field and potential in the drift and amplification regions of the detector. This paper describes the hands on learning process and in depth research accomplishment that the undergraduate students have undertaken in the ten weeks of intensive summer learning. A detailed Maxwell simulation for the gas electron multiplier (GEM) and the micro mesh gaseous (MICROMEGAS) detectors are shown and experimental results of the double GEM fluorescence x-ray detector are depicted.