gebhart/patrepeval huggingface dataset:
An Interferometric Reflectance Imaging Sensor for Point of Care Viral Diagnostics (2013)

The use of in vitro diagnostic devices is transitioning from the laboratory to the primary care setting to address early disease detection needs. Time critical viral diagnoses are often made without support due to the experimental time required in today's standard tests. Available rapid point of care (POC) viral tests are less reliable, requiring a follow-on confirmatory test before conclusions can be drawn. The development of a reliable POC viral test for the primary care setting would decrease the time for diagnosis leading to a lower chance of transmission and improve recovery. The single particle interferometric reflectance imaging sensor (SP-IRIS) has been shown to be a sensitive and specific-detection platform in serum and whole blood. This paper presents a step towards a POC viral assay through a SP-IRIS prototype with automated data acquisition and analysis and a simple, easy-to-use software interface. Decreasing operation complexity highlights the potential of SP-IRIS as a sensitive and specific POC diagnostic tool. With the integration of a microfluidic cartridge, this automated instrument will allow an untrained user to run a sample-to-answer viral assay in the POC setting.
ChemInform Abstract: A Cerium(III) Modification of the Peterson Reaction: Methylenation of Readily Enolizable Carbonyl Compounds. (1987)

Abstract Addition of the reagent (II) to the enolizable carbonyl compounds (I) gives the products (III) in the presence of cerium chloride with yields superior to those obtained with other reagents.
Acid–Base Catalysis and Crystal Structures of a Least Evolved Ancestral GFP-like Protein Undergoing Green-to-Red Photoconversion (2013)

In green-to-red photoconvertible fluorescent proteins, a three-ring chromophore is generated by the light-activated incorporation of a histidine residue into the conjugated π-system. We have determined the pH-rate profile and high- and low-pH X-ray structures of a least evolved ancestor (LEA) protein constructed in the laboratory based on statistical sequence analysis. LEA incorporates the minimal number of substitutions necessary and sufficient for facile color conversion and exhibits a maximal photoconversion quantum yield of 0.0015 at pH 6.1. The rate measurements provide a bell-shaped curve, indicating that the reaction is controlled by the two apparent pKa values, 4.5 ± 0.2 and 7.5 ± 0.2, flanking the chromophore pKa of 6.3 ± 0.1. These data demonstrate that the photoconversion rate of LEA is not proportional to the A-form of the GFP-like chromophore, as previously reported for Kaede-type proteins. We propose that the observed proton dissociation constants arise from the internal quadrupolar charge network consisting of Glu222, His203, Glu148, and Arg69. Increased active site flexibility may facilitate twisting of the chromophore upon photoexcitation, thereby disrupting the charge network and activating the Glu222 carboxylate for the abstraction of a proton from a carbon acid. Subsequently, the proton may be delivered to the Phe64 carbonyl by a hydrogen-bonded network involving Gln42 or by means of His65 side chain rotations promoted by protein breathing motions. A structural comparison of LEA with the nonphotoconvertible LEA-Q42A variant supports a role for Gln42 either in catalysis or in the coplanar preorganization of the green chromophore with the His65 imidazole ring.
On-line range verification for proton beam therapy using spherical ionoacoustic waves with resonant frequency (2020)

In contrast to conventional X-ray therapy, proton beam therapy (PBT) can confine radiation doses to tumours because of the presence of the Bragg peak. However, the precision of the treatment is currently limited by the uncertainty in the beam range. Recently, a unique range verification methodology has been proposed based on simulation studies that exploit spherical ionoacoustic waves with resonant frequency (SPIREs). SPIREs are emitted from spherical gold markers in tumours initially introduced for accurate patient positioning when the proton beam is injected. These waves have a remarkable property: their amplitude is linearly correlated with the residual beam range at the marker position. Here, we present proof-of-principle experiments using short-pulsed proton beams at the clinical dose to demonstrate the feasibility of using SPIREs for beam-range verification with submillimetre accuracy. These results should substantially contribute to reducing the range uncertainty in future PBT applications.
Thermal Shock Synthesis of Metal Nanoclusters within On-the-Fly Graphene Particles (2019)

Metal nanoclusters (1-10 nm) have drawn great attention because of their potential applications including energy storage, catalysis, nanomedicine, and electronic devices. However, manufacturing ultrasmall metal nanoparticles at high concentrations in an unaggregated state is not a solved problem. Here, we report an aerosol-based thermal shock technique for in situ synthesis of well-dispersed metal nanoclusters in on-the-fly graphene aerosols. A rapid thermal shock to the graphene aerosol has been used to nucleate and grow the metal nanoclusters with subsequent quenching to freeze the newly formed nanoclusters in the graphene aerosol matrix. A characteristic time analysis comparison with the experiment shows that the nanocluster formation is governed by nucleation and subsequent surface growth and that the graphene retards coagulation, enabling unaggregated metal nanoclusters. The method is generic, and we show the formation of sub-10 nm Ni, Co, and Sn nanoclusters. This continuous aerosol-based thermal shock technique offers considerable potential for the scalable synthesis of well-dispersed and uniform metal nanoclusters stabilized within a host matrix. As an example of potential application, we demonstrate very favorable catalytic properties.
Two-stage facet color images filtering (2002)

Two algorithms for linear filtering of the colour map are presented. The first algorithm is based on independent filtering of colour channels. The second one is constructed by taking into account the cross correlation of channels. The advantages of the algorithms are shown and a brief review of further scientific activity is given.
Supplemental Figure 2 from First-in-Human Trial of a Novel Anti-Trop-2 Antibody-SN-38 Conjugate, Sacituzumab Govitecan, for the Treatment of Diverse Metastatic Solid Tumors (2023)

&lt;p&gt;Time to progression in relation to the immunohistological score in 16 patients with diverse cancers enrolled in the sacituzumab govitecan trial who provided archival tissue specimens.&lt;/p&gt;
Targeting a neoantigen derived from a common TP53 mutation (2021)

<i>TP53</i> (tumor protein p53) is the most commonly mutated cancer driver gene, but drugs that target mutant tumor suppressor genes, such as <i>TP53</i>, are not yet available. Here, we describe the identification of an antibody highly specific to the most common <i>TP53</i> mutation (R175H, in which arginine at position 175 is replaced with histidine) in complex with a common human leukocyte antigen-A (HLA-A) allele on the cell surface. We describe the structural basis of this specificity and its conversion into an immunotherapeutic agent: a bispecific single-chain diabody. Despite the extremely low p53 peptide-HLA complex density on the cancer cell surface, the bispecific antibody effectively activated T cells to lyse cancer cells that presented the neoantigen in vitro and in mice. This approach could in theory be used to target cancers containing mutations that are difficult to target in conventional ways.
Molecular medical approaches for alleviating infertility and understanding assisted reproductive technologies. (1996)

Fertilization is a precisely orchestrated cascade of events that results in the union of paternal and maternal genomes and in the establishment of mitotic potential of the zygote. To initiate embryonic development, the structures of the fertilizing sperm have to be disassembled and transformed into zygotic components by interactions with the cytoplasm of the egg. These interactions include the decondensation of the sperm nucleus into male pronucleus, the assembly of the zygotic centrosome, and the gathering of centrosomal proteins and sperm aster microtubules around the sperm centriole. Both the formation of the male pronucleus and the assembly of the zygotic centrosome are crucial steps required for pronuclear apposition and genomic union. The discovery of previously undetected fertilization failures that are due to defects in the assembly of the zygotic centrosome, abnormal pronuclear development, and compromised cytoskeletal dynamics enforces the development of new diagnostic strategies. Moreover, the introduction of new methods of infertility treatments, such as intracytoplasmic sperm injection and round spermatid nucleus injection into assisted human reproductive technology programs, emphasizes our lack of understanding of the cellular and molecular basis of human fertilization and evokes the need for additional experimentation. These efforts, however, are compromised by the sensitive nature of human embryo research and thus are severely restricted. Animal models that are reliable and cost-effective and that feature the characteristics of human fertilization have therefore been sought. Rodents such as the rat, mouse, and hamster are poor models owing to their maternal inheritance of the zygotic centrosome that is in strong contrast with the biparentally contributed assembly of the human zygotic centrosome during fertilization. Although rabbits are similar to humans from the standpoint of mitotic potential inheritance, information on postfertilization events in rabbits are lacking. Nonhuman primates represented by the rhesus monkey proved to be a reliable model for human in vitro fertilization and intracytoplasmic sperm injection, an advantage that is further emphasized by phyllogenetic similarity. In situations in which the high cost of primate research does not allow for large-scale experimentation (i.e., when large numbers of oocytes and embryos are needed), ruminants would be an ideal solution. Represented by the cow and sheep, domestic ruminants feature a fertilization strategy similar to that of the human. In addition, large numbers of gametes can be obtained wherever farms and slaughterhouses are accessible. Moreover, the detailed information on ruminant fertilization is strengthened by years of research and well-defined reproductive technology aimed at increasing the productivity of farm animals. Ruminants and rhesus monkeys have been extensively studied, and the data from these studies have been extrapolated in order to propose new strategies for the diagnosis and treatment of human infertility.
Controlling biofilm formation with nitroxide functional surfaces (2019)

Nitroxide functional polymer coatings with inherent antibiofilm activity are introduced as an avenue to combat bacterial biofilm contamination of medical devices.
Zuclopenthixol, D1/D2 antagonist, for treatment of chronic aggressive schizophrenia and psychotic oligophrenic patients (1998)

An open label trial was conducted to study the efficacy of zuclopenthixol decanoate, a D(1)/D(2) antagonist, in the treatment of chronic (> 10 years) neuroleptic-resistant aggressive schizophrenia (n = 10) and psychotic oligophrenic patients (n = 6). A significant reduction was noted in the Brief Psychiatric Rating Scale score, especially in the clusters of hostility-suspiciousness and excitement. After many years of seclusion, ten of the 16 patients were transferred to an open psychiatric department and were allowed to visit their families.
Resource Sharing Among mmWave Cellular Service Providers in a Vertically\n Differentiated Duopoly (2017)

With the increasing interest in the use of millimeter wave bands for 5G\ncellular systems comes renewed interest in resource sharing. Properties of\nmillimeter wave bands such as massive bandwidth, highly directional antennas,\nhigh penetration loss, and susceptibility to shadowing, suggest technical\nadvantages to spectrum and infrastructure sharing in millimeter wave cellular\nnetworks. However, technical advantages do not necessarily translate to\nincreased profit for service providers, or increased consumer surplus. In this\npaper, detailed network simulations are used to better understand the economic\nimplications of resource sharing in a vertically differentiated duopoly market\nfor cellular service. The results suggest that resource sharing is less often\nprofitable for millimeter wave service providers compared to microwave cellular\nservice providers, and does not necessarily increase consumer surplus.\n
Human organs-on-chips for disease modelling, drug development and personalized medicine (2022)

The failure of animal models to predict therapeutic responses in humans is a major problem that also brings into question their use for basic research. Organ-on-a-chip (organ chip) microfluidic devices lined with living cells cultured under fluid flow can recapitulate organ-level physiology and pathophysiology with high fidelity. Here, I review how single and multiple human organ chip systems have been used to model complex diseases and rare genetic disorders, to study host-microbiome interactions, to recapitulate whole-body inter-organ physiology and to reproduce human clinical responses to drugs, radiation, toxins and infectious pathogens. I also address the challenges that must be overcome for organ chips to be accepted by the pharmaceutical industry and regulatory agencies, as well as discuss recent advances in the field. It is evident that the use of human organ chips instead of animal models for drug development and as living avatars for personalized medicine is ever closer to realization.
A Versatile Synthetic Approach to Peptidyl Privileged Structures Using a “Safety-Catch” Linker (2005)

Peptidyl privileged structures have been widely used by many groups to discover biologically active molecules. In this context, privileged substructures are used as "hydrophobic anchors", to which peptide functionality is appended to gain specificity. Utilization of this concept has led to the discovery of many different active compounds at a wide range of biological receptors. A synthetic approach to these compounds has been developed on a "safety-catch" linker that allows rapid preparation of large libraries of these molecules. Importantly, amide bond formation/cleavage through treatment with amines is the final step; it is a linker strategy that allows significant diversification to be easily incorporated, and it only requires the inclusion of an amide bond. In addition, chemistry has been developed that permits the urea moiety to be inserted at the N-terminus of the peptide, allowing the same set of amines (either privileged substructures or amino acid analogues) to be used at both the N- and C-termini of the molecule. To show the robustness of this approach, a small library of peptidyl privileged structures were synthesized, illustrating that large combinatorial libraries can be synthesized using these technologies.
Constrained Control of Input Delayed Systems With Partially Compensated Input Delays (2020)

Abstract Control Barrier Functions (CBFs) have become popular for enforcing — via barrier constraints — the safe operation of nonlinear systems within an admissible set. For systems with input delay(s) of the same length, constrained control has been achieved by combining a CBF for the delay free system with a state predictor that compensates the single input delay. Recently, this approach was extended to multi input systems with input delays of different lengths. One limitation of this extension is that barrier constraint adherence can only be guaranteed after the longest input delay has been compensated and all input channels become available for control. In this paper, we consider the problem of enforcing constraint adherence when only a subset of input delays have been compensated. In particular, we propose a new barrier constraint formulation that ensures that when possible, a subset of input channels with shorter delays will be utilized for keeping the system in the admissible set even before longer input delays have been compensated. We include a numerical example to demonstrate the effectiveness of the proposed approach.
Epitope prediction for oligomer‐selective antibodies in tau and Aβ (2020)

Abstract Background Previous studies of Alzheimer’s disease (AD) pathology point to cytotoxic tau as a cause of neuronal cell death, which is induced or exacerbated by soluble misfolded Aβ oligomers. Soluble misfolded species of both tau and Aβ are both observed to propagate cell‐to‐cell. A method for identifying antibodies to tau and Aβ that are conformationally‐selective to propagative misfolded oligomeric forms, and which also have low affinity to isolated monomers or, particularly for Aβ, low affinity to fibrils, is thus a highly desired goal that holds significant promise for AD therapy. Method We have developed a novel computational platform to identify epitopes that may be selectively exposed on oligomers. Epitope prediction ideally uses an experimentally determined fibril structure as input, but the method alters this structure using molecular dynamics, to more accurately model the regions that may be exposed on soluble oligomers. Both primary sequence and structural conformation are taken into account: The epitope should be conformationally‐distinct from those conformations presented in the functional healthy protein. Epitope scaffolding is then employed to optimize the presentation of the epitope in animal immunizations, so that the resulting antibodies are predicted to be selective to misfolded oligomeric forms. Result Oligomer‐specific epitope predictions for tau and for Aβ have been used to raise preclinical antibodies that have selectivity for pathogenic tau and Aβ species. In vitro SPR measurements confirmed selective binding to synthetic oligomers and soluble pre‐formed fibrils (PFFs), vs. native healthy protein. As well, the antibodies showed little immunoreactivity toplaque or vascularAβ deposits via immunohistochemistry, while SEC fractionation of AD brain homogenate shows selective binding to toxic dimers, tetramers and dodecamers, in contrast to aducanumab and bapineuzumab. Tau antibodies recognized tau from AD brain extract, and inhibited seeding activity in a FRET assay. Aβ antibodies alleviated the cognitive deficits caused by oligomers in mouse NOR studies. Conclusion Lead antibodies to tau and Aβ developed using rationally designed conformational epitopes are likely to achieve greater therapeutic potency by selectively targeting soluble toxic oligomers, and reducing the risk of target distraction and ARIA.
Thermal Management and Processing Optimization for 3D Multi-layer Stacked ICs (2019)

3D ICs integration has shown significant advantage in performance enhancement and power reduction. One of the key components in 3D integration technology is to stack multi-layer thinned ICs to make a reliable electrical and mechanical connection. Thermo compression bonding (TCB) has been used to manufacture 3D ICs due to its capability to bond fine pitch micro bumps. However, it has been a challenge for TCB process to control the temperature over the bonding interfaces and it increases its complexity when multi bonding interface are bonded at once. In this paper we use integrated thermo sensor to investigate temperature gradient during TCB for multi die stacking. The real time temperature measurements are combined with finite element modeling (FEM). The calibrated model is used to explore temperature in bonding interfaces that are not accessible through measurement and enhance the understanding of heat transfer during the TCB process for multi die stacks.
Amelioration By Tempol Of The Hypertensive And Baroreflex Depressant Effects Of Cyclosporine In Conscious Rats: Role Of Cardiac Autonomic Control (2010)

Previous studies including ours showed that cyclosporine (CSA) causes hypertension and baroreflex dysfunction. This study tested the hypothesis that increased oxidative damage mediates CSA effects. Experiments were undertaken in rats to investigate the effects of individual and combined 7‐day treatments with CSA (25 mg/kg/day) and tempol (superoxide dismutase mimetic, 100 mg/kg/day) on BP, reflex HR responses to peripherally mediated pressor and depressor responses, and biomarkers of oxidative stress. The role of cardiac autonomic control in cyclosporine‐tempol interaction was also investigated. CSA elevates blood pressure and reduced reflex bradycardic (phenylephrine) and tachycardic (sodium nitroptrusside) responses. The ability of muscarinic (atropine) or β‐adrenoceptors (propranolol) blockade to reduce reflex HR responses was reduced in CSA‐treated rats, suggesting impairment by CSA of cardiac autonomic control. Concurrent administration of tempol abolished CSA‐induced hypertension, baroreflex dysfunction, and autonomic impairment. Tempol also reversed the CSA‐induced increases in aortic and brainstem nitrite/nitrate and malondialdehyde and decreases in aortic superoxide dismutase. These findings implicate oxidative stress, at peripheral and central sites, in CSA‐induced hypertension and baroreflex dysfunction.
RETROGRADE RENAL PELVIC ACCESS SHEATH TO FACILITATE FLEXIBLE URETEROSCOPIC LITHOTRIPSY FOR THE TREATMENT OF UROLITHIASIS IN A HORSESHOE KIDNEY (2000)

No AccessJournal of UrologyCase Reports1 Oct 2000RETROGRADE RENAL PELVIC ACCESS SHEATH TO FACILITATE FLEXIBLE URETEROSCOPIC LITHOTRIPSY FOR THE TREATMENT OF UROLITHIASIS IN A HORSESHOE KIDNEY CASSIO ANDREONI, ANDREW J. PORTIS, and RALPH V. CLAYMAN CASSIO ANDREONICASSIO ANDREONI , ANDREW J. PORTISANDREW J. PORTIS , and RALPH V. CLAYMANRALPH V. CLAYMAN View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)67158-3AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "RETROGRADE RENAL PELVIC ACCESS SHEATH TO FACILITATE FLEXIBLE URETEROSCOPIC LITHOTRIPSY FOR THE TREATMENT OF UROLITHIASIS IN A HORSESHOE KIDNEY." The Journal of Urology, 164(4), pp. 1290–1291 References 1 : Ureteroscopic management of intrarenal calculi. J Urol1998; 159: 1139. Link, Google Scholar 2 : Clinical implications of clinically insignificant stone fragments after extracorporeal shock wave lithotripsy. J Urol1996; 155: 1186. Link, Google Scholar From the Department of Surgery, Division of Urologic Surgery and Department of Radiology, Washington University School of Medicine, St. Louis, Missouri© 2000 by American Urological Association, Inc.FiguresReferencesRelatedDetailsCited byGinsberg D, Boone T, Cameron A, Gousse A, Kaufman M, Keays E, Kennelly M, Lemack G, Rovner E, Souter L, Yang C and Kraus S (2021) The AUA/SUFU Guideline on Adult Neurogenic Lower Urinary Tract Dysfunction: Diagnosis and EvaluationJournal of Urology, VOL. 206, NO. 5, (1097-1105), Online publication date: 1-Nov-2021.Assimos D (2017) Re: Ureteroscopic Urinary Stone Treatment among Patients with Renal Anomalies: Patient Characteristics and Treatment OutcomesJournal of Urology, VOL. 199, NO. 3, (604-604), Online publication date: 1-Mar-2018.RAJ G, AUGE B, WEIZER A, DENSTEDT J, WATTERSON J, BEIKO D, ASSIMOS D and PREMINGER G (2018) Percutaneous Management of Calculi Within Horseshoe KidneysJournal of Urology, VOL. 170, NO. 1, (48-51), Online publication date: 1-Jul-2003.WU N, AUGE B and PREMINGER G (2018) SIMPLIFIED URETERAL STENT PLACEMENT WITH THE ASSISTANCE OF A URETERAL ACCESS SHEATHJournal of Urology, VOL. 166, NO. 1, (206-208), Online publication date: 1-Jul-2001. Volume 164Issue 4October 2000Page: 1290-1291 Advertisement Copyright & Permissions© 2000 by American Urological Association, Inc.Keywordskidney calculikidneyureteroscopyMetricsAuthor Information CASSIO ANDREONI More articles by this author ANDREW J. PORTIS More articles by this author RALPH V. CLAYMAN More articles by this author Expand All Advertisement PDF downloadLoading ...