gebhart/patrepeval huggingface dataset:
Image Exchange: IHE and the Evolution of Image Sharing (2008)

The sharing of radiologic images has become a fundamental part of radiology services and is essential for delivering high-quality care. Film is quickly becoming obsolete as a means of transporting and sharing large volumes of imaging data. Image sharing has evolved from film to transportable media (eg, compact disks) to direct electronic exchange over the Internet. The latter two means of image sharing have associated work flow-related and technical challenges for which solutions are being developed. Integrating the Healthcare Enterprise (IHE) provides a standards-based approach to the development of robust, universally accepted solutions. Several IHE profiles have been developed to provide a framework for current image sharing efforts. The Philadelphia and New Jersey Health Information Exchanges and the Canada Health Infoway represent efforts to apply IHE technical profiles to facilitate the secure and confidential exchange of electronic images over the Internet. The research community is concomitantly developing solutions that solve image exchange issues that are specific to research (eg, the sharing of deidentified data) but that might also be encountered in the general population. The personal health record is a more recent development that may provide consumers with direct control over the process of sharing images electronically with their healthcare providers.
Function of Phenylalanine 259 and Threonine 314 within the Substrate Binding Pocket of the Juvenile Hormone Esterase ofManduca sexta (2010)

Juvenile hormone (JH) is a key insect developmental hormone that is found at low nanomolar levels in larval insects. The methyl ester of JH is hydrolyzed in many insects by an esterase that shows high specificity for JH. We have previously determined a crystal structure of the JH esterase (JHE) of the tobacco hornworm Manduca sexta (MsJHE) [Wogulis, M., Wheelock, C. E., Kamita, S. G., Hinton, A. C., Whetstone, P. A., Hammock, B. D., and Wilson, D. K. (2006) Biochemistry 45, 4045-4057]. Our molecular modeling indicates that JH fits very tightly within the substrate binding pocket of MsJHE. This tight fit places two noncatalytic amino acid residues, Phe-259 and Thr-314, within the appropriate distance and geometry to potentially interact with the alpha,beta-unsaturated ester and epoxide, respectively, of JH. These residues are highly conserved in numerous biologically active JHEs. Kinetic analyses of mutants of Phe-259 or Thr-314 indicate that these residues contribute to the low K(M) that MsJHE shows for JH. This low K(M), however, comes at the cost of reduced substrate turnover. Neither nucleophilic attack of the resonance-stabilized ester by the catalytic serine nor the availability of a water molecule for attack of the acyl-enzyme intermediate appears to be a rate-determining step in the hydrolysis of JH by MsJHE. We hypothesize that the release of the JH acid metabolite from the substrate binding pocket limits the catalytic cycle. Our findings also demonstrate that chemical bond strength does not necessarily correlate with how reactive the bond will be to metabolism.
Requirement of Myeloid Cells for Axon Regeneration (2008)

The role of CD11b+ myeloid cells in axonal regeneration was assessed using axonal injury models and CD11b-TK(mt-30) mice expressing a mutated HSV-1 thymidine kinase (TK) gene regulated by the myeloid-specific CD11b promoter. Continuous delivery of ganciclovir at a sciatic nerve lesion site greatly decreased the number of granulocytes/inflammatory monocytes and macrophages in the distal stump of CD11b-TK(mt-30) mice. Axonal regeneration and locomotor function recovery were severely compromised in ganciclovir-treated CD11b-TK(mt-30) mice. This was caused by an unsuitable growth environment rather than an altered regeneration capacity of neurons. In absence of CD11b+ cells, the clearance of inhibitory myelin debris was prevented, neurotrophin synthesis was abolished, and blood vessel formation/maintenance was severely compromised in the sciatic nerve distal stump. Spinal cord-injured axons also failed to regenerate through peripheral nerve grafts in the absence of CD11b+ cells. Therefore, myeloid cells support axonal regeneration and functional recovery by creating a growth-permissive milieu for injured axons.
USE of CHITOSAN COATING to REDUCE WATER LOSS and MAINTAIN QUALITY of CUCUMBER and BELL PEPPER FRUITS (1991)

The effect of chitosan coating (1.0 and 1.5% w/v) on the storability of bell pepper and cucumber fruits stored at 13 and 20C (RH 85%) was determined by monitoring the weight loss, respiration and quality: Chitosan coating markedly reduced the weight loss in both bell pepper and cucumber at both temperatures. Increasing the concentration of chitosan from 1.0 to 1.5% (w/v) resulted in a significantly greater weight retention in both fruits. In addition, coating cucumber and bell pepper with chitosan reduced the respiration rate, loss of color, wilting and fungal infection. the mechanism by which chitosan coating delayed senescence in bell pepper and cucumber is most likely due to its ability to alleviate water stress.
The Octahedral Manipulator: Geometry and Mobility (1998)

In most of the practical six-actuator, in-parallel manipulators, the octahedral form is either taken as it stands or is approximated. Yet considerable theoretical attention is paid in the literature to more general forms. Here we touch on the general form, and describe some aspects of its behavior that vitiate strongly against its adoption as a pattern for a realistic manipulator. We reach the conclusion that the structure for in-parallel manipulators must be triangulated as fully as possible, so leading to the octahedral form. In describing some of the geometrical properties of the general octahedron, we show how they apply to manipulators. We examine in detail the special configurations at which the 6 x 6 matrix of leg lines is singular, presenting results from the point of view of geometry in preference to analysis. In extending and enlarging on some known properties, a few behavioral surprises materialize. In studying special configurations, we start with the most general situation, and every other case derives from this. Our coverage is more comprehensive than any that we have found. We bring to light material that is, we think, of significant use to a designer.
Prognosis (2005)

Enhancements are foreseen in EPR instrumentation and application of EPR to biological systems. The need for educating future researchers about the use of EPR is emphasized.
Safe caching in a distributed file system for network attached storage (2002)

In a distributed file system built on network attached storage, client computers access data directly from shared storage, rather than submitting I/O requests through a server. Without a server marshaling access to data, if a computer fails or becomes isolated in a network partition while holding locks on cached data objects, those objects become inaccessible to other computers until a locking authority can guarantee that the lock holder will not again directly access these data. We describe a server that acts as the locking authority and implements a lease-based protocol for revoking access to data objects locked by an isolated or failed computer. When a lease expires, the server can be assured that the client no longer acts on locked data, and can safely redistribute locks to other clients. During normal operation, this protocol invokes no message overhead, and uses no memory and performs no computation at the locking authority.
[Protocols for the chemotherapy of solid tumors: should we increase or reduce?]. (1984)

Contrary to the treatment of leukemia and lymphoma which is clearly defined, for most solid tumors the place, the type and the intensity of treatments remain under discussion. Experimental results are available to prove the benefit of various drug combinations in which doses, routes of treatment, schedule and number of cycles are carefully evaluated. However considering the difficulties in testing all the combinations which are possible and the lack of trust in the predictive value of experimental studies, it is generally according to clinical results that escalation or reduction of chemotherapy are decided, At the present time and for many solid tumors, escalation is predominating due to the low effectiveness of the current drugs we have at our disposal. It is only in the case of curable solid tumors (for example: carcinoma of the testis, choriocarcinoma) that a reduction phase is possible and this behaviour is justified in avoiding the iatrogenic effects of chemotherapy. Many examples of escalation and reduction are given in clinical cancer chemotherapy.
Physical and timing verification of subwavelength-scale designs: I. Lithography impact on MOSFETs (2003)

Subwavelength lithography at low contrast, or low-k1 factor, leads to new requirements for design, design analysis, and design verification techniques. These techniques must account for inherent physical circuit feature distortions resulting from layout pattern-dependent design-to-silicon patterning processes in this era. These distortions are unavoidable, even in the presence of sophisticated Resolution Enhancement Technologies (RET), and are a 'fact-of-life’ for the designer implementing nanometer-scale designs for the foreseeable low-k1 future. The consequence is that fabricated silicon feature shapes and dimensions are in general printed with far less fidelity in comparison to the designer’s desired layout than in past generations and that the designer must consider design within significantly different margins of geometry tolerance. Traditional (Mead-Conway originated) WYSIWYG (what you see is what you get) design methodologies, assume that the designer’s physical circuit element shapes are accurate in comparison to the corresponding shapes on the real fabricated IC, and uses design rules to verify satisfactory fabrication compliance, as the input for both interconnect parasitic loading calculations and to transistor models used for performance simulation. However, these assumptions are increasingly poor ones as k1 decreases to unprecidented levels -- with concomitant increase in patterned feature distortion and fabrication yield failure modes. This paper explores a new paradigm for nanometer-scale design, one in which more advanced models of critical low-k1 lithographic printing effects are incorporated into the design flow to improve upon yield and performance verification accuracy. We start with an analysis of a complex 32-bit adder block circuit design to determine systematic changes in gate length, width and shape variations for each MOSFET in the circuit due to optical proximity effects. The physical gate dimensions for all, as predicted by the simulations, are then incorporated into the circuit simulation models and netlist (schematic) and are used to calculate the changes in critical parametric yield factors such as timing and power consumption in the circuit behavior. These functional consequences create a manufacturability tolerance requirement that relates to function and parametric yield, not just physical manufacturability. We then explore the improvements in functional attributes and manufacturability that arise from systematic correction of these distortions by RET including; simulation-driven model-based OPC, alternating-aperture PSM (altPSM), and altPSM+OPC. This analysis is just one dimension of a systmatic methodology that incorporates lithographic effects into a design for manufacturing (DFM) scheme. The benefits promise dramatically improved silicon-signoff verification, predictive performance and yield analysis, and more cost-effective application of RET.
How keratoconus influences optical performance of the eye (2008)

Using a statistical description of keratoconus (KC) topography, schematic eye models of various KC conditions are constructed to study their optical influence on visual performance. The cone shape, protruding height and extent, and distance from the visual zone are independently investigated with the three-dimensional optical eye-modeling and ray-tracing techniques. The subsequent spherical equivalent (SE), cylinder, together with residual high-order ocular aberrations, are examined and related to each separated variable. The results show that myopic nature of SE is greatly dominated by the location of the cone. The cylinder is determined by the cone shape when the cone is inside the visual zone. It is dominated by the cone location when the cone is away from visual axis. The least myopic meridian always falls on the cone direction, and the high-order aberrations strongly relate to the cone dimension. This study investigates KC cone effect on optical quality and provides comprehension of clinical observations.
Bioinformatics tools as a way to select microbial strains for fermented food products (2019)

1. Introduction\nFermented foods are complex biological ecosystems, harbouring diverse microbial communities which contribute to the quality of these food products. In most industrial processes, these communities are advisedly chosen as starter culture for their adaptation to: (i) the substrates to be fermented (milk, vegetable) (ii) the process (°C, O2, NaCl) and (iii) the desired overall quality of the food product in terms of texture, flavour, nutrition and health benefits. For this purpose, technological properties have been mainly assessed by a time-consuming in vitro screening. We hypothesis that the huge amount of bibliographic and microbial genomic data available in public databases would enable an in silico preselection of the strains of interest before wet laboratory screening experiments.\n2. Objectives\nOur aim was to provide (i) adapted bioinformatic tools to mine the diversity of microbial technological properties and metabolisms (ii) a strategy to preselect strains based on their phenotypes and on their genetic potential (sugar utilization, aroma production).\n3. Material and Methods\nWe used a bioanalysis approach to provide insight into the presence of enzyme-encoding genes responsible for targeted technological properties. KEGG, Metacyc, NCBI and CAZY databases were queried by a search on enzyme numbers, names and sequence alignments. We developed Florilege (http://migale.jouy.inra.fr/Florilege/), a database of microbial phenotypes based on text-mining to gather microbial growth conditions.\n4. Results\nCombining both approaches, we set up a bioinformatic preselection of lactic acid bacteria able to degrade sugar from milk, cereal or legume based juice to develop yogurt-like products. Database queries provided a list of microbial species with genes encoding key targeted enzymes. A set of preselected anaerobic, mesophilic and thermophilic strains has been successfully screened on different milk and juice in our wet laboratory providing potential new starter strains.\n5. Conclusion\nThe developed tools and the strategy can be usefully applied to other domains like bioremediation and white biotechnology.\n
Sampling of Grain and Seed to Estimate the Adventitious Presence of Biotechnology-Derived Seeds in a Lot (2015)

Sampling and subsequent analysis are essential steps to assess the characteristics of grain and seed lots. In this article, the basic principles of sampling statistics and how to apply them to grain or seed are described for analysts who do not have significant training in statistics. Although these principles are described in the context of sampling grain and seed to test for the presence of low concentrations of genetically modified organisms (GMOs), they can be applied to the sampling of grain or seed for any characteristic.
Assembly of a Pentagonal Polyoxomolybdate Building Block, [Mo6O21]6–, into Crystalline MoV Oxides (2012)

Abstract The building‐block assembly of polyoxometalates to form crystalline MoV‐based metal oxides is presented. Mixing of (NH 4 ) 6 Mo 7 O 24 and VOSO 4 in water with a pH value higher than 1.7 produced the ball‐shaped polyoxometalate [Mo 72 V 30 O 282 (H 2 O) 56 (SO 4 ) 12 ] 36– ({Mo 72 V 30 }) with 12 pentagonal [Mo 6 O 21 ] 6– polyoxomolybdate units connected to 30 [V=O] 2+ units, which was detected by using UV/Vis, Raman, and IR spectroscopy. Hydrothermal reaction of the precursor containing {Mo 72 V 30 } produced crystalline orthorhombic or trigonal MoV oxides. These oxides contain the pentagonal Mo unit in the crystal structure. The results indicate that the pentagonal polyoxomolybdate unit produced in the reaction precursor assembles with other Mo and V ions to form crystalline orthorhombic and trigonal MoV oxides.
High-Pressure Synthesis and Characterization of β-GeSe—A Six-Membered-Ring Semiconductor in an Uncommon Boat Conformation (2017)

Two-dimensional materials have significant potential for the development of new devices. Here we report the electronic and structural properties of β-GeSe, a previously unreported polymorph of GeSe, with a unique crystal structure that displays strong two-dimensional structural features. β-GeSe is made at high pressure and temperature and is stable under ambient conditions. We compare it to its structural and electronic relatives α-GeSe and black phosphorus. The β form of GeSe displays a boat conformation for its Ge-Se six-membered ring ("six-ring"), while the previously known α form and black phosphorus display the more common chair conformation for their six-rings. Electronic structure calculations indicate that β-GeSe is a semiconductor, with an approximate bulk band gap of Δ ≈ 0.5 eV, and, in its monolayer form, Δ ≈ 0.9 eV. These values fall between those of α-GeSe and black phosphorus, making β-GeSe a promising candidate for future applications. The resistivity of our β-GeSe crystals measured in-plane is on the order of ρ ≈ 1 Ω·cm, while being essentially temperature independent.
Nontarget Analysis of Oxygenates in Catalytic Fast Pyrolysis Biocrudes by Supercritical Fluid Chromatography High-Resolution Mass Spectrometry (2018)

Catalytic fast pyrolysis (CFP) biocrudes can comprise up to 30 wt % of oxygen content in compounds such as polyphenols, acids, carbonyls, and anhydrosugars and thus require upgrading by, e.g., hydrotreatment, to produce transport fuels. The chemical characterization of phenolic and acidic compounds in biocrudes is of great importance to optimize the CFP process. In this study, an analytical workflow is proposed for nontarget chemical fingerprinting analysis of CFP biocrudes using supercritical fluid chromatography high-resolution mass spectrometry (SFC-HRMS) with negative electrospray ionization (ESI–), followed by multivariate data analysis. The method was developed and tested on five biocrude samples from loblolly pine (Pinus taeda) with varying oxygen content (14.9–28.8 wt % wet basis) due to different CFP conditions. The pixel-based analysis displayed chemical variation between all samples. Twenty-four regions of interest were tentatively identified, including mono- and polyphenols, fatty acids, and methylated and methoxylated phenols. The identification workflow and MS/MS analysis were prioritized on the peaks with the highest relative concentration. The developed SFC-ESI–-HRMS method shows high repeatability and analyzed oxygen-containing compounds with hydroxyl and/or carboxyl moieties in combination with other moieties of up to 400 Da.
Empowering Global Chemical Biology at the Dawn of the New Decade (2020)

On January 22-24, 2020, scientific luminaries across the far-flung corners of chemical biology gathered in Geneva, Switzerland, to deliver their latest and greatest discoveries in the field. Generously supported by the Swiss National Science Foundation (SNSF), our academic partners, and industrial and journal sponsors, this chemical biology symposium in our opinion will remain memorable for several years to come, not only because of the diversity in scientific topics delivered by our invited eminent speakers as detailed herein, but it is also one-of-a-kind conference which reflected multidimensional balance-balance in age and gender, across these speakers. Such a remarkable speaker line-up doubtless attracted >200 attendees from academia and industry in and around Switzerland and beyond, representing a huge swathe of subfields of science interfacing chemistry and biology. Poster presentations from students and postdocs further spotlighted the exciting diversity in the field: spanning biosynthesis, optochemical genetics, genetic code expansion, lipid chemical biology, redox perturbation, microfluidics screening, membrane signaling, immune modulation, DNA circuits, and synthetic and computational biology. This notable heterogeneity in scientific topics also went hand-in-hand with the diverse representations of student/postdoc trainees from 56 institutions covering 14 countries worldwide, allowing us to witness science as a truly global enterprise.
Benchmarking Geometric Deep Learning for Cortical Segmentation and Neurodevelopmental Phenotype Prediction (2021)

Abstract The emerging field of geometric deep learning extends the application of convolutional neural networks to irregular domains such as graphs, meshes and surfaces. Several recent studies have explored the potential for using these techniques to analyse and segment the cortical surface. However, there has been no comprehensive comparison of these approaches to one another, nor to existing Euclidean methods, to date. This paper benchmarks a collection of geometric and traditional deep learning models on phenotype prediction and segmentation of sphericalised neonatal cortical surface data, from the publicly available Developing Human Connectome Project (dHCP). Tasks include prediction of postmenstrual age at scan, gestational age at birth and segmentation of the cortical surface into anatomical regions defined by the M-CRIB-S atlas. Performance was assessed not only in terms of model precision, but also in terms of network dependence on image registration, and model interpretation via occlusion. Networks were trained both on sphericalised and anatomical cortical meshes. Findings suggest that the utility of geometric deep learning over traditional deep learning is highly task-specific, which has implications for the design of future deep learning models on the cortical surface. The code, and instructions for data access, are available from https://github.com/Abdulah-Fawaz/Benchmarking-Surface-DL .
Microalbuminuria and essential hypertension: renal and cardiovascular implications (1997)

Microalbuminuria continues to receive attention in patients with hypertension, even if they do not have diabetes mellitus. The attention appears deserved, because microalbuminuria has emerged as an important risk factor for left ventricular hypertrophy, myocardial infarction, stroke, peripheral vascular disease and retinopathy, independent of blood pressure. Microalbuminuria may be a useful measurement during pregnancy and appears particularly indicated in following up women who develop pre-eclampsia during pregnancy. In addition to diabetes, increased blood pressure and age, the smoking habit appears to be the most important factor contributing to microalbuminuria, although other influences including uranium exposure have been implicated. We need to learn more about the mechanisms of microalbuminuria, particularly in non-diabetic hypertensive patients. Microalbuminuria is potentially reversible. All antihypertensive agents appear to reduce microalbuminuria. In diabetic patients, angiotensin-converting enzyme inhibitor therapy is effective in reducing renal disease progression, even in the absence of hypertension. Antioxidant therapy may be effective. Stopping smoking should be the initial antioxidant measure.