gebhart/patrepeval huggingface dataset:
High performance model based image reconstruction (2016)

Computed Tomography (CT) Image Reconstruction is an important technique used in a wide range of applications, ranging from explosive detection, medical imaging to scientific imaging. Among available reconstruction methods, Model Based Iterative Reconstruction (MBIR) produces higher quality images and allows for the use of more general CT scanner geometries than is possible with more commonly used methods. The high computational cost of MBIR, however, often makes it impractical in applications for which it would otherwise be ideal. This paper describes a new MBIR implementation that significantly reduces the computational cost of MBIR while retaining its benefits. It describes a novel organization of the scanner data into super-voxels (SV) that, combined with a super-voxel buffer (SVB), dramatically increase locality and prefetching, enable parallelism across SVs and lead to an average speedup of 187 on 20 cores.
On the Loss of Injectant and Apparent Dispersivity in Single-Well Push-Pull Tests Influenced by Natural Drift (2010)

In a previous article, a semi-analytical stream-line based model was developed for single-well push-pull tests in stratified reservoirs subject to natural drift. Based on that model, this article gives the theoretical maximum injection phase duration giving conservative injectant production, in a single-layer reservoir with natural drift. In addition, an analytical expression for the single-layer apparent dispersivity due to natural drift is given. Finally, it is shown how the large-scale apparent dispersivities observed in experimental data from a stratified aquifer may be predicted by constructing a production profile using the estimated single-layer apparent dispersivities.
Chronic Vagal Nerve Stimulation Rescues Sympathetic Control of the Heart following Myocardial Infarction (2022)

Cardiac injury, such as myocardial infarction (MI), leads to neurohormonal activation and autonomic remodeling, resulting in reflexive sympathoexcitation and parasympathetic dysfunction, which further contribute to progression of disease. The purpose of this study was to determine whether chronic cervical vagal nerve stimulation (VNS) influences MI‐associated changes in cardiac sympathetic function. Yucatan minipigs were divided into control (n=6), chronic MI (n=7), and chronic MI + chronic VNS (n=8) groups. VNS therapy was delivered to the right cervical vagus nerve and systematically titrated to an optimal intensity based on heart rate dynamics (5Hz, 2.1±0.3mA, 250μs, 17.5% duty cycle) using telemetry in the conscious state. Chronic MI was created using percutaneous embolization of the left anterior descending coronary artery with polystyrene beads under fluoroscopy (Figure 1A). VNS therapy was started 2 days following MI, and the animals maintained for 6‐8 weeks. At terminal study, we evaluated hemodynamic responses to graded bilateral sympathetic chain stimulation (BSS). Left ventricular (LV) strips encompassing regions of scar, border zone, and normal myocardium were fixed in 10% formalin, embedded in paraffin, sectioned, and studied using Masson's trichrome stain (Figure 1B‐C). Structural changes at the peri‐infarct area were scored (0‐3) for myocyte morphology and presence of hypertrophy or myocytolysis. Animals with MI alone exhibited spontaneous ventricular arrhythmias, including two that experienced sudden cardiac death (Figure 1D). At terminal study, there were no significant differences in baseline systolic function among groups. Moderate (4Hz) and high (10Hz) intensity BSS increased LV contractility (dp/dt max ) in all groups (Figure 2A‐B); however, evoked changes were significantly reduced in the chronic MI compared to control or MI + VNS groups. While control animals displayed evidence of contractile reserve at 10Hz vs 4Hz (1297±266 mmHg/s, p=0.03), chronic MI animals did not (631.9±264 mmHg/s, p=0.11), which was improved with chronic VNS therapy (1027±160.6 mmHg/s, p&lt;0.01, Figure 2C). Chronic VNS therapy also significantly reduced MI‐associated structural remodeling in the peri‐infarct area, including the degree of myocytolysis and dysmorphic myocytes (structural abnormality index 0.6±0.2 vs 1.8±0.2, p&lt;0.01). Our findings suggest that chronic VNS ameliorates sympathetic functional remodeling following myocardial infarction and improves cardiac mechanical performance in response to simulated stress. Furthermore, chronic VNS reduces pathologic myocardial remodeling at the peri‐infarct zone, potentially stabilizing the resultant ventricular scar.
Repurposing Clinical Molecule Ebselen to Combat Drug Resistant Pathogens (2015)

Without a doubt, our current antimicrobials are losing the battle in the fight against newly-emerged multidrug-resistant pathogens. There is a pressing, unmet need for novel antimicrobials and novel approaches to develop them; however, it is becoming increasingly difficult and costly to develop new antimicrobials. One strategy to reduce the time and cost associated with antimicrobial innovation is drug repurposing, which is to find new applications outside the scope of the original medical indication of the drug. Ebselen, an organoselenium clinical molecule, possesses potent antimicrobial activity against clinical multidrug-resistant Gram-positive pathogens, including Staphylococcus, Streptococcus, and Enterococcus, but not against Gram-negative pathogens. Moreover, the activity of ebselen against Gram-positive pathogens exceeded those activities determined for vancomycin and linezolid, drugs of choice for treatment of Enterococcus and Staphylococcus infections. The minimum inhibitory concentrations of ebselen at which 90% of clinical isolates of Enterococcus and Staphylococcus were inhibited (MIC90) were found to be 0.5 and 0.25 mg/L, respectively. Ebselen showed significant clearance of intracellular methicillin-resistant S. aureus (MRSA) in comparison to vancomycin and linezolid. We demonstrated that ebselen inhibits the bacterial translation process without affecting mitochondrial biogenesis. Additionally, ebselen was found to exhibit excellent activity in vivo in a Caenorhabditis elegans MRSA-infected whole animal model. Finally, ebselen showed synergistic activities with conventional antimicrobials against MRSA. Taken together, our results demonstrate that ebselen, with its potent antimicrobial activity and safety profiles, can be potentially used to treat multidrug resistant Gram-positive bacterial infections alone or in combination with other antibiotics and should be further clinically evaluated.
Cross-sectional neck response of a total human body FE model during simulated frontal and side automobile impacts (2013)

Human body finite element (FE) models are beginning to play a more prevalent role in the advancement of automotive safety. A methodology has been developed to evaluate neck response at multiple levels in a human body FE model during simulated automotive impacts. Three different impact scenarios were simulated: a frontal impact of a belted driver with airbag deployment, a frontal impact of a belted passenger without airbag deployment and an unbelted side impact sled test. Cross sections were created at each vertebral level of the cervical spine to calculate the force and moment contributions of different anatomical components of the neck. Adjacent level axial force ratios varied between 0.74 and 1.11 and adjacent level bending moment ratios between 0.55 and 1.15. The present technique is ideal for comparing neck forces and moments to existing injury threshold values, calculating injury criteria and for better understanding the biomechanical mechanisms of neck injury and load sharing during sub-injurious and injurious loading.
A Framework to Report the Production of Renewable Diesel from Algae (2010)

Recently, algae have received significant interest as a potential feedstock for renewable diesel (such as biodiesel), and many researchers have attempted to quantify this potential. Some of these attempts are less useful because they have not incorporated specific values of algal lipid content, have not included processing inefficiencies, or omitted processing steps required for renewable diesel production. Furthermore, the associated energy, materials, and costs requirements are sometimes omitted. The accuracy and applicability of these estimates can be improved by using data that are more specific, including all relevant information for renewable diesel production, and by presenting information with more relevant metrics. To determine whether algae are a viable source for renewable diesel, three questions that must be answered are (1) how much renewable diesel can be produced from algae, (2) what is the financial cost of production, and (3) what is the energy ratio of production? To help accurately answer these questions, we propose an analytical framework and associated nomenclature system for characterizing renewable diesel production from algae. The three production pathways discussed in this study are the transesterification of extracted algal lipids, thermochemical conversion of algal biomass, and conversion of secreted algal oils. The nomenclature system is initially presented from a top-level perspective that is applicable to all production pathways for renewable diesel from algae. Then, the nomenclature is expanded to characterize the production of renewable diesel (specifically, biodiesel) from extracted algal lipids in detail (cf. Appendix 2). The analytical framework uses the presented nomenclature system and includes three main principles: using appropriate reporting metrics, using symbolic notation to represent unknown values, and presenting results that are specific to algal species, growth conditions, and product composition.
ChemInform Abstract: [2.2]Paracyclophane‐Based Monophosphine Ligand for Palladium‐Catalyzed Cross‐Coupling Reactions of Aryl Chlorides. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Deficient nitric oxide signalling impairs skeletal muscle growth and performance: involvement of mitochondrial dysregulation (2014)

Our results indicate that nNOSμ/NO is required to regulate key homeostatic mechanisms in skeletal muscle, namely mitochondrial bioenergetics and network remodelling, UPR(mt) and autophagy. These events are likely associated with nNOSμ-dependent impairments of muscle fibre growth resulting in a deficit of muscle performance.
Supplementary Tables from Early Noninvasive Detection of Response to Targeted Therapy in Non–Small Cell Lung Cancer (2023)

&lt;p&gt;The supplementary tables for "Early noninvasive detection of response to targeted therapy in non-small cell lung cancer" report clinical characteristics of patients analyzed (1), serial timepoints analyzed (2), genes analyzed (3), a summary of genomic analyses (4), somatic sequence alterations detected in cfDNA (5), somatic structural alterations detected in cfDNA (6), and blood cell proliferation alterations detected in cfDNA (7).&lt;/p&gt;
Optimal current patterns in impedance imaging (2002)

This paper reports the effect on the distinguishability and system noise of using a complete set of optimal current patterns in an impedance imaging system. Experiments performed using agar and saline phantoms with different conductivity distributions showed an improvement in the distinguishability and in the image contrast.
FluidMedia: an offline peer-to-peer media transaction system (2002)

The FluidMedia system provides a convenient means to legally transfer copyrighted digital media. Its ability to support off-line sales transactions and authentication of media access rights allows system users great flexibility in the way they access and distribute media, yet still provides strong control over piracy for content distributors. Furthermore, the FluidMedia system supports transaction policies that provide economic incentives to system users to distribute media.
A New Statistical Model for Gate Array Routing (1983)

A new statistical model for routing of gate arrays is described. The model takes into consideration the effect of gate utilization of wiring area requirement. Model computed wiring area estimates suggest that it is better (in terms of area and wire length) to use higher utilization and a relatively large number of tracks than low utilization and smaller number of tracks. This is shown to be consistent with the results of two experiments.
Crumple Zones: Absorbing Attack Effects Before They Become a Problem (2011)

Abstract : A specific and currently relevant issue motivating the notion of ruggedized software is the confluence of the threat of cyber attacks and our increased dependence on software systems in enterprise as well as tactical situations. Software services that are essential for mission success must not only withstand normal wear and tear, stresses and accidental failures, they also must endure the stresses and failures caused by malicious activities and continue to remain usable. The Crumple Zone (CZ), a software shock absorber that absorbs attack effects before they cause significant system failures, is an architectural construct that we have developed and are maturing iteratively. We argue that the CZ is an important building block for constructing ruggedized software for supporting network-centric operations. In this paper we discuss the CZ in the context of Service-Oriented Architecture (SOA) and describe a configuration that has been realized and demonstrated.
A double mutant of Pseudomonas putida JLR11 deficient in the synthesis of the nitroreductase PnrA and assimilatory nitrite reductase NasB is impaired for growth on 2,4,6‐trinitrotoluene (TNT) (2006)

Summary Pseudomonas putida JLR11 can grow on 2,4,6‐trinitrotoluene (TNT) as the sole nitrogen source. We created nasB (nitrite reductase), pnrA (nitroaromatic reductase) and pnrA nasB mutants and tested their growth with TNT as the sole N source. The nasB and pnrA mutants grew at a reduced rate on TNT, whereas the double nasB pnrA mutant did not. This suggests that P. putida JLR11 carries out multiple enzymatic attacks on TNT‐releasing nitrite and/or ammonium. The PnrA nitroreductase plays a key role in the reduction of TNT to 2,6‐dinitro‐4‐hydroxylaminotoluene and the subsequent release of ammonium for growth.
Altered interleukin-1 and tumor necrosis factor production and secretion during pyrogenic tolerance to LPS in rabbits (1994)

Rabbits were injected intravenously with 10 micrograms/kg of endotoxin [lipopolysaccharide (LPS)] on days 0, 1, and 7, and rectal temperatures were monitored. The febrile responses were compared with circulating levels of interleukin-1 beta (IL-1 beta) and tumor necrosis factor (TNF) and in vitro synthesis of these cytokines by peripheral blood mononuclear cells (PBMC) isolated just before the injection of LPS. Fever after the first LPS injection was biphasic on day 0, attenuated and monophasic after the second LPS injection on day 1, and augmented after third injection of LPS on day 7. On day 1, circulating TNF and IL-1 beta levels were significantly (P < 0.05) decreased compared with those on days 0 and 7. Similarly, TNF and IL-1 beta synthesis by LPS-stimulated PBMC were significantly reduced on day 1. On day 7, cellular synthesis and secretion of IL-1 beta were significantly increased compared with that on day 0. A significant positive correlation was observed between fever index and total in vitro IL-1 beta synthesis by LPS-stimulated PBMC (r = 0.866, P = 0.001). These data demonstrate that pyrogenic tolerance in the rabbit after a single LPS injection is associated with decreased circulating IL-1 beta and TNF levels as well as decreased production of these cytokines in vitro. In addition, the pyrogenic hyperresponsiveness to LPS after 7 days is associated with increased synthesis and secretion of IL-1 beta from PBMC in vitro.
Data from Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features (2023)

&lt;div&gt;Abstract&lt;p&gt;The Notch pathway is frequently altered in head and neck squamous cell carcinomas (HNSCC); however, the clinical significance of &lt;i&gt;NOTCH1&lt;/i&gt; dysregulation is poorly understood. This study was designed to characterize expression of the transcriptionally active NOTCH1 intracellular domain (NICD1) in HNSCCs and evaluate its association with &lt;i&gt;NOTCH1&lt;/i&gt; mutation status and clinical parameters. IHC for NICD1 was performed on 79 previously sequenced archival HNSCCs with known &lt;i&gt;NOTCH1&lt;/i&gt; mutation status. Three distinct immunohistochemical staining patterns were identified: positive/peripheral (47%), positive/nonperipheral (34%), and negative (19%). NICD1 expression was associated with &lt;i&gt;NOTCH1&lt;/i&gt; mutation status (&lt;i&gt;P&lt;/i&gt; &lt; 0.001). Most &lt;i&gt;NOTCH1&lt;/i&gt;–wild-type tumors were peripheral (55%), whereas mutated &lt;i&gt;NOTCH1&lt;/i&gt; tumors were most commonly negative (47%). Nonperipheral tumors were more likely than peripheral tumors to have extracapsular spread [adjusted odds ratio (aOR), 16.01; 95% confidence interval (CI), 1.92–133.46; &lt;i&gt;P&lt;/i&gt; = 0.010] and poor differentiation (aOR, 5.27; 95% CI, 0.90–30.86; &lt;i&gt;P&lt;/i&gt; = 0.066). Negative staining tumors tended to be poorly differentiated (aOR, 24.71; 95% CI, 1.53–399.33; &lt;i&gt;P&lt;/i&gt; = 0.024) and were less likely to be human papillomavirus (HPV) positive (aOR, 0.043; 95% CI, 0.001–1.59; &lt;i&gt;P&lt;/i&gt; = 0.087). &lt;i&gt;NOTCH1&lt;/i&gt; mutagenesis was significantly associated with HPV status, with &lt;i&gt;NOTCH1&lt;/i&gt;–wild-type tumors more likely to be HPV positive than &lt;i&gt;NOTCH1&lt;/i&gt;-mutated tumors (aOR, 19.06; 95% CI, 1.31–276.15; &lt;i&gt;P&lt;/i&gt; = 0.031). &lt;i&gt;TP53&lt;/i&gt; disruptive mutations were not associated with NICD1 expression or &lt;i&gt;NOTCH1&lt;/i&gt; mutation. In conclusion, NICD1 is expressed in three distinct patterns in HNSCC that are significantly associated with high-risk features. These findings further support a dual role for &lt;i&gt;NOTCH1&lt;/i&gt; as both tumor suppressor and oncogene in HNSCC. Further research is necessary to clarify the role of &lt;i&gt;NOTCH1&lt;/i&gt; in HNSCC and understand the clinical and therapeutic implications therein. &lt;i&gt;Cancer Prev Res; 8(4); 287–95. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Comparison of house dust mite sensitization profiles in allergic adults from Canada, Europe, South Africa and USA (2021)

Sensitization profiles to HDM allergens differ considerably among distinct geographic areas, with Der p 7 and Der p 23 being major sensitizers in South Africa. Such heterogeneity should be taken into account in the diagnosis and treatment of HDM-allergic patients.
Increased complement activation 3 to 6 h after trauma is a predictor of prolonged mechanical ventilation and multiple organ dysfunction syndrome: a prospective observational study (2021)

Complement activation 3 to 6 h after injury was a better predictor of prolonged mechanical ventilation and multiple organ dysfunction syndrome than admission TCC. Our data suggest that the greatest surge of complement activation is found within the first 6 h after injury, and we argue that this time period should be in focus in the design of future experimental studies and clinical trials using complement inhibitors.
Comment on the Origin of the 2019 Novel Coronavirus (2020)

Analysis of all genetic, epidemiological and geophysical and astrophysical data suggest the alternate hypothesis that nCoV-2019 arrived via a meteorite, presumed carbonaceous meteorite, that struck North East China on October 11 2019. We then assume the viral debris and particles then made land fall in the Wuhan and related regions about a month to six weeks later resulting in first cases of the viral pneumonia caused by nCoV-2019 emerging in Wuhan regions late November 2019-early December 2019.
Back Cover: Bicatalytic Multistep Reactions En Route to the One‐Pot Total Synthesis of Complex Molecules: Easy Access to Chromene and 1,2‐Dihydroquinoline Derivatives from Simple Substrates (ChemCatChem 1/2017) (2017)

The Cover shows the ingredients for a one-pot/5-steps reaction catalyzed by Au nanoparticles under O2 and a simple base such as pyrrolidine.In their Communication, P. D. Giorgi et al. describe an efficient one-pot process to convert simple starting materials such as allylic alcohols into valuable substituted chromenes and dihydroquinolines. The reaction proceeds through an oxidation/hetero-Michael addition/aldolization/crotonization and involves salicylaldehyde and aminobenzaldehyde derivatives as partners, which could also be generated in situ from the corresponding benzyl alcohols. More information can be found in the Communication by P. D. Giorgi et al. on page 70 in Issue 1, 2017 (DOI: 10.1002/cctc.201600925).
Dopant-Free Channel Transistor with Punchthrough Control Region under Source and Drain (1994)

A dopant-free channel metal-oxide-semiconductor field-effect transistor (MOSFET) featuring the punchthrough control region of moderate dopant concentrations under the source and the drain is proposed. This device structure is based on a new concept that the channel contains no appreciable ionized dopants at which electric field lines originating from the drain terminate whereas field lines from the drain mainly terminate at ionized dopants in the punchthrough control under the drain. The two-dimensional simulation analysis suggests that this device has good punchthrough control and consequently can be scaled down to 0.05 µm gate length. In this device, punchthrough can be suppressed by controlling the fringe effect of the pn junction formed between the drain and the punchthrough control.