gebhart/patrepeval huggingface dataset:
Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research (2014)

<b>Significance:</b> The colonization of wounds by specific microbes or communities of microbes may delay healing and/or lead to infection-related complication. Studies of wound-associated microbial communities (microbiomes) to date have primarily relied upon culture-based methods, which are known to have extreme biases and are not reliable for the characterization of microbiomes. Biofilms are very resistant to culture and are therefore especially difficult to study with techniques that remain standard in clinical settings. <b>Recent Advances:</b> Culture-independent approaches employing next-generation DNA sequencing have provided researchers and clinicians a window into wound-associated microbiomes that could not be achieved before and has begun to transform our view of wound-associated biodiversity. Within the past decade, many platforms have arisen for performing this type of sequencing, with various types of applications for microbiome research being possible on each. <b>Critical Issues:</b> Wound care incorporating knowledge of microbiomes gained from next-generation sequencing could guide clinical management and treatments. The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing. <b>Future Directions:</b> As DNA sequencing technology progresses, platforms will continue to produce longer reads and more reads per run at lower costs. A major future challenge is to implement these technologies in clinical settings for more precise and rapid identification of wound bioburden.
Hormonal interventions with psychopharmacological potential: an overview. (1997)

The better understanding of how hormones modulate cognition and behavior is associated with the application of hormones as psychotropic medications. Several natural and synthetic hormones are used as adjuncts to antidepressant medications or as treatments in their own right. We discuss pharmacotherapeutical aspects of estrogen, thyroid hormones, cortisol suppressors, and melatonin as examples of current trends in the field. In addition to the putative roles of these hormones in the treatment of affective disorders, estrogen might also be used as a cognition-enhancer, and both estrogen and thyroid hormones might have roles as mood stabilizers. The psychotropic effects of melatonin have recently received significant attention, but the exact role of that hormone still needs to be clarified.
Chemical Defense in Ascidians of the <i>Didemnidae</i> Family (2002)

Fluorescent analogues (DB1 and TA1) of the secondary metabolites didemnin B (DB) and tamandarin A (TA) were synthesized to investigate the potential chemical defense mechanisms of tunicates in the family Didemnidae. These compounds were found to alter predator-prey relations. Five species of freshwater fish and one marine fish, the damselfish Amphiprion ocellaris, were acclimated to a diet of mosquito larvae. Fish showed an immediate, negative reaction to mosquito larvae treated with >/=5 ng of DB1 or TA1, with consumption of larvae resulting in regurgitation. Both freshwater and marine fish learned to avoid tainted prey by associating species of larvae with "distaste". Distaste for a given organism also arose when depsipeptides DB1 or TA1 were transferred to the fish from the surrounding medium. Fluorescence microscopy in fish indicated that a similar processing and localization followed ingestion and absorption of DB1 or TA1. Fluorescent labeling of DB or TA provided an ideal tool to conduct short-term studies of predator-prey relationships between fish and marine invertebrate larvae.
Electroactive poly(sulfobetaine-3,4-ethylenedioxythiophene) (PSBEDOT) with controllable antifouling and antimicrobial properties (2015)

This paper reports a multifunctional zwitterionic poly(sulfobetaine-3,4-ethylenedioxythiophene) (PSBEDOT), which could be facilely synthesized by electropolymerization in aqueous solution. The PSBEDOT surface exhibits excellent conductivity, stability and switchable antifouling/antimicrobial properties. It shows great promise for applications in organic bioelectronics. This new material may significantly increase the performance and service life, minimize the foreign body reaction, improve the biocompatibility and reduce the infection of bio-electronic devices.
Mitochondrial genome organization and expression associated with cytoplasmic male sterility in sunflower (<i>Helianthus annuus)</i> (1991)

A comparative investigation of the organization and expression of the mitochondrial genome in fertile and cytoplasmic male sterile (CMS) sunflower (Helianthus annuus) has been undertaken. A region of mitochondrial genome variation between the two phenotypes has been located in the 3' flanking region of the gene encoding the alpha subunit of the F1 ATPase (atpA). Physical mapping and sequence analysis have been used to show that a rearrangement involving an inversion and an insertion has occurred immediately downstream of the atpA coding region in the mitochondrial DNA from sterile sunflower. This rearrangement has resulted in the creation of a new open reading frame (ORFc) which is co-transcribed with atpA in sterile sunflower. In organello labelling of mitochondrial translation products from the two types of sunflower shows that a 15 kDa protein is synthesized by the mitochondria from sterile sunflower but not by those from fertile plants. The ORFc sequence could encode this 15 kDa protein which may be causally related to the CMS phenotype.
Molecular Cloning and Genomic Analysis of Mouse Galβ1,3GalNAc-specific GalNAc α2,6-Sialyltransferase (1996)

cDNA and genomic clones encoding mouse Galbeta1, 3GalNAc-specific GalNAc alpha2,6-sialyltransferase (ST6GalNAc II) were isolated, and the structure organization of the gene was determined. The predicted amino acid sequence is 57.4% identical to the chick ST6GalNAc II sequence but 33.8% identical to the chick ST6GalNA I (GalNAc alpha2, 6-sialyltransferase) sequence. The ST6GalNAc II gene is constitutively expressed in various mouse tissues but highly expressed in lactating mammary gland and adult testis. The gene contains nine exons spanning about 25 kilobases of genomic DNA and encodes a messenger RNA of 1995 nucleotides. Primer extension and S1 nuclease protection analysis of submaxillary gland mRNA showed that the transcription of the ST6GalNAc II gene starts from 68 nucleotides upstream from the translation start site. Characterization of 5'-flanking genomic regions indicated that the Galbeta1,3GalNAc-specific GalNAc alpha2,6-sialyltransferase promoter is embedded in a G+C-rich domain and contains no TATA or CAAT box but has putative binding sites for transcription factors Sp1 and AP-2. Transient transfection experiments involving luciferase reporter genes demonstrated promoter activity in NIH3T3 cells.
Curcumin Opens Cystic Fibrosis Transmembrane Conductance Regulator Channels by a Novel Mechanism That Requires neither ATP Binding nor Dimerization of the Nucleotide-binding Domains (2006)

Cystic fibrosis transmembrane conductance regulator (CFTR) chloride channels are essential mediators of salt transport across epithelia. Channel opening normally requires ATP binding to both nucleotide-binding domains (NBDs), probable dimerization of the two NBDs, and phosphorylation of the R domain. How phosphorylation controls channel gating is unknown. Loss-of-function mutations in the CFTR gene cause cystic fibrosis; thus, there is considerable interest in compounds that improve mutant CFTR function. Here we investigated the mechanism by which CFTR is activated by curcumin, a natural compound found in turmeric. Curcumin opened CFTR channels by a novel mechanism that required neither ATP nor the second nucleotide-binding domain (NBD2). Consequently, this compound potently activated CF mutant channels that are defective for the normal ATP-dependent mode of gating (e.g. G551D and W1282X), including channels that lack NBD2. The stimulation of NBD2 deletion mutants by curcumin was strongly inhibited by ATP binding to NBD1, which implicates NBD1 as a plausible activation site. Curcumin activation became irreversible during prolonged exposure to this compound following which persistently activated channels gated dynamically in the absence of any agonist. Although CFTR activation by curcumin required neither ATP binding nor heterodimerization of the two NBDs, it was strongly dependent on prior channel phosphorylation by protein kinase A. Curcumin is a useful functional probe of CFTR gating that opens mutant channels by circumventing the normal requirements for ATP binding and NBD heterodimerization. The phosphorylation dependence of curcumin activation indicates that the R domain can modulate channel opening without affecting ATP binding to the NBDs or their heterodimerization.
Apolipoprotein J: a membrane policeman? (1992)

Apolipoprotein (apo)J is unique among secreted lipid transport proteins with structural features in common both with other apolipoproteins and with components of the complement system. Its two disulfide-linked subunits are produced by post-translational cleavage of a single polypeptide chain. Moreover, apoj is present in distinct subclasses of high and very-high-density plasma lipoproteins which have aα electrophoretic mobility. We propose that apoj acts in both surface-bound and diffusible forms to maintain cell membrane integrity by using its hydrophobic-binding domains to police the membrane and extracellular space against potentially harmful hydrophobic molecules. This hypothesis is founded on the restriction of apoj gene expression to specific cell types, its known lipid-binding capacity, its association with cell membranes, its capacity to inhibit the membrane attack complement complex, and its marked induction in degenerative situations.
A direct method for the simultaneous and optimal multidimensional models registration (2002)

An innovative solution of the global multidimensional registration problem for a set of partial object models is introduced and explained. The method, based on the classical tie-point concept, is capable to directly and optimally align models indefinitely rotated, translated and scaled. The pre-registration is carried out in an automatic way without the need of initial manual superimposition nor of approximate starting values of the transformation parameters. Registration algorithms implementing the singular value decomposition of matrix products of limited size are used in every step of the process. The procedure is based on the algorithms of the Procrustes analysis. One consequent advantage is that there are no space dimensions restrictions. This is particularly helpful for laser scanning and digital photogrammetry applications, where a set of attributes associated to the different tie-points (i.e. CYMK or RGB color components and intensity) can be used in conjunction with the corresponding Cartesian coordinate values. This connection can improve the registration reliability of range-colored images, matching simultaneously geometry, nature and aspect. The numerical experiments carried out confirm the advantages of the multidimensional approach proposed.
Ternäre Halogenide vom Typ A<sub>3</sub>MX<sub>6</sub>. I A<sub>3</sub>YCl<sub>6</sub> (A = K, NH<sub>4</sub>, Rb, Cs): Synthese, Strukturen, Thermisches Verhalten. Über einige analoge Chloride der Lanthanide (1992)

Abstract Chloride vom Typ A 3 MCl 6 (A = K, Rb, Cs; M = Y, TbLu) werden durch Umsetzung der Trichloride MCl 3 mit Alkalichloriden ACl in evakuierten Quarzglas‐Ampullen bei 850–900°C dargestellt, (NH 4 ) 3 YCl 6 nach der “Ammoniumchlorid‐Methode”. Die Röntgenstrukturanalyse an einem Einkristall von Rb 3 YCl 6 (monoklin, C2/c (Nr. 15), Z = 8, a = 2583(1) pm, b = 788,9(4) pm, c = 1283,9(7) pm, β = 99,63(4)°, R = 0,062, R w = 0,050) ergab Isotypie zu Cs 3 BiCl 6 . Ausgehend vom Elpasolith‐Typ (K 2 NaAlF 6 ) werden Cs 3 BiCl 6 und nahe verwandte Strukturen (K 3 MoCl 6 , In 2 Cl 3 ) mit dem Modell dichtest gepackter Schichten beschrieben. Für die zu Rb 3 YCl 6 isotypen Chloride Rb 3 MCl 6 (M = Y, TbLu), sowie Cs 3 YCl 6 und Cs 3 ErCl 6 werden Gitterkonstanten angegeben. Das “System” (K, NH 4 , Rb, Cs)YCl 6 wurde mittels DTA und Heiz‐Guinier‐Aufnahmen untersucht.
Research Strategies in the Study of the Pro-Oxidant Nature of Polyphenol Nutraceuticals (2011)

Polyphenols of phytochemicals are thought to exhibit chemopreventive effects against cancer. These plant-derived antioxidant polyphenols have a dual nature, also acting as pro-oxidants, generating reactive oxygen species (ROS), and causing oxidative stress. When studying the overall cytotoxicity of polyphenols, research strategies need to distinguish the cytotoxic component derived from the polyphenol per se from that derived from the generated ROS. Such strategies include (a) identifying hallmarks of oxidative damage, such as depletion of intracellular glutathione and lipid peroxidation, (b) classical manipulations, such as polyphenol exposures in the absence and presence of antioxidant enzymes (i.e., catalase and superoxide dismutase) and of antioxidants (e.g., glutathione and N-acetylcysteine) and cotreatments with glutathione depleters, and (c) more recent manipulations, such as divalent cobalt and pyruvate to scavenge ROS. Attention also must be directed to the influence of iron and copper ions and to the level of polyphenols, which mediate oxidative stress.
Passive Immunotherapy for Anthrax Toxin Mediated by an Adenovirus Expressing an Anti-Protective Antigen Single-Chain Antibody (2004)

In the 2001 U.S. bioterror attacks, 33,000 individuals required postexposure prophylaxis, 18 subjects contracted anthrax (11 inhalation, 7 cutaneous), and despite optimal medical therapy, 5 deaths resulted. Rapid protection against anthrax is required in a bioterrorism scenario; this study describes an in vivo gene transfer-based therapy that uses a human adenovirus (Ad)-based vector (AdalphaPAscAb) encoding a single-chain antibody directed against protective antigen (PA), a critical component of Bacillus anthracis lethal toxin. Following AdalphaPAscAb administration to mice, anti-PA single-chain antibody and anti-PA neutralizing activity were detected in serum over a 2-week period. Substantial survival advantage from anthrax lethal toxin was conferred by AdalphaPAscAb following administration from 1 to 14 days prior to toxin challenge, compared to no survival associated with an Ad vector expressing a control single-chain antibody. Passive immunotherapy with an Ad-based vector may be a rapid, convenient approach for protecting a susceptible population against anthrax, including use as an adjunct to antibiotic therapy.
Incorporating Weather Updates for Public Transportation Users of Recommendation Systems (2016)

This work presents a system for augmenting the functionality of Yelp-like recommendation sites by enabling users to search for places bounded by travel-time when using public transportation, and modifying recommendations based on updated weather conditions. Using public transport, although is cheaper and efficient, entails that only fixed places of boarding/exiting may be used which, in turn, implies walking to (from) a particular location from (to) a given station. Given the impact of the weather on the mood and activities, preferences for a certain type of services may need to be dynamically adjusted based on the current weather or the near-future forecast, modulo travel-routes to preferred locations. In this work, we develop a model to predict a user's preferred mode of transport (car, or public transit) from their old check-ins and incorporate the weather context into the recommendation process. We use event-based modeling to control the extent of walking depending on user-defined tolerance information and live weather conditions. We implemented a web application (both desktop and mobile platforms), utilizing existing tools such as Google Maps Direction API and Open Weather Map API for retrieving real-time information.
Dynamic Interstitial Cell Response during Myocardial Infarction Predicts Resilience to Rupture in Genetically Diverse Mice (2020)

Cardiac ischemia leads to the loss of myocardial tissue and the activation of a repair process that culminates in the formation of a scar whose structural characteristics dictate propensity to favorable healing or detrimental cardiac wall rupture. To elucidate the cellular processes underlying scar formation, here we perform unbiased single-cell mRNA sequencing of interstitial cells isolated from infarcted mouse hearts carrying a genetic tracer that labels epicardial-derived cells. Sixteen interstitial cell clusters are revealed, five of which were of epicardial origin. Focusing on stromal cells, we define 11 sub-clusters, including diverse cell states of epicardial- and endocardial-derived fibroblasts. Comparing transcript profiles from post-infarction hearts in C57BL/6J and 129S1/SvImJ inbred mice, which displays a marked divergence in the frequency of cardiac rupture, uncovers an early increase in activated myofibroblasts, enhanced collagen deposition, and persistent acute phase response in 129S1/SvImJ mouse hearts, defining a crucial time window of pathological remodeling that predicts disease outcome.
SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS (2015)

The characterization of amyloid-beta peptide (Aβ) oligomer forms and structures is crucial to the advancement in the field of Alzheimer´s disease (AD). Here we report a critical evaluation of two methods used for this purpose, namely sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), extensively used in the field, and ion mobility coupled to electrospray ionization mass spectrometry (ESI-IM-MS), an emerging technique with great potential for oligomer characterization. To evaluate their performance, we first obtained pure cross-linked Aβ40 and Aβ42 oligomers of well-defined order. Analysis of these samples by SDS-PAGE revealed that SDS affects the oligomerization state of Aβ42 oligomers, thus providing flawed information on their order and distribution. In contrast, ESI-IM-MS provided accurate information, while also reported on the chemical nature and on the structure of the oligomers. Our findings have important implications as they challenge scientific paradigms in the AD field built upon SDS-PAGE characterization of Aβ oligomer samples.
Cooperative Intersection Collision Avoidance System (CICAS): Signalized Left Turn Assist and Traffic Signal Adaptation (2010)

The Cooperative Intersection Collision Avoidance (CICAS) program is a multi-year, cooperative research program including federal, state, academic, and industry partners. The goal of the research program is to use ITS technologies to address the problem of intersection crashes. The program is funded through an 80/20 cost share, typically split between the U.S. Department of Transportation (D.O.T.) and a local state D.O.T. The program began in 2003, and has been divided into three functional segments based on crash type. The largest programmatic segment is CICAS-V (Violation) which is led by CAMP, with support from researchers at Virginia Tech, and aims to address the problem of straight crossing path collisions which tend to be the result of stop sign or stop light violators. A second programmatic segment is CICAS-SSA (Stop Sign Assist) which is led by the Minnesota D.O.T., with support from researchers at the University of Minnesota, and aims to address the problems associated with crossing or entering a high-speed, rural road from a stop sign at a minor road. The final programmatic segment is CICAS-SLTA (Signalized Left Turn Assist) which is lead by Caltrans, with support from the California PATH Program (Partners for Advanced Transit and Highways) at the University of California, Berkeley. This CICAS-SLTA segment aims to address crashes caused by vehicles making left turns at signalized intersections where there is no protected left-turn signal.This report focuses on the activities related to the CICAS-SLTA program segment. It builds upon work that was performed during earlier segments (Task Orders 5600, 5601 and 6607) which included the previous Intersection Decision Support (IDS) project and CICAS. The CICAS-SLTA project is currently continuing research in the areas of sensor testing, field data collection, human factors data collection and testing, and warning algorithm design and simulation. The project aimes scheduled to lead to the design of a Field Operational Test (FOT) ready system and detailed FOT work plan, depending on the success of this and a subsequent effort.
Swine, Control of Hog Lice on Brood Sows, 1978 (1981)

Abstract Two tests were conducted in Buckingham County, Virginia, from June ’78 to Aug ’78 on brood sows. Two rates of GX-118, 1:2 parts water and 1:5 parts water, were compared to pre-treatment counts and untreated check animals. GX-118 contains 11.6% Prolate (phosmet) which equals 1 lb per gallon active ingredient. Both dilutions were applied as a pour-on. Animals were treated along the backline from the neck area to the hip area. Approximately 1 oz/cwt of body weight was applied to each animal by means of a calibrated dipper.
Recoverable polyimides. (II): DSC studies of copolymers from 4, 4′‐dithiodianiline bismaleimide (DTDA‐BM) and aromatic diamines (1990)

Abstract Interest in the recently reported polyimide resins containing disulfide bonds, which could be cleaved by reduction for reprocessing and/or recovery, prompted the present investigation of polymers and copolymers of the DTDA bismaleimide previously described. Differential scanning calorimetry (DSC) studies were carried out to identify the structures, curing conditions and modifications of reduced products of potential value for industrial applications. Results have shown that selected cured copolymers of DTDA bismaleimide with aromatic diamines can be solubilized by reduction and reset in subsequent reactions to yield thermosets of satisfactory properties.
FLAME: Macroscopic imaging with microscopic resolution. Optical biopsy of human skin (2020)

Abstract We introduce a compact, fast large area multiphoton exoscope (FLAME) system with enhanced molecular contrast for macroscopic imaging of human skin with microscopic resolution. A versatile imaging platform with multiple modes of operation for comprehensive analysis of live or resected thick human skin tissue, it produces 3D images that encompass sub-mm 2 to cm 2 scale areas of tissue within minutes. The FLAME imaging platform, which expands on a design recently introduced by our group, features deep learning, additional scanning hardware elements and time-resolved single photon counting detection to uniquely allow fast discrimination and 3D virtual staining of melanin. We demonstrate its performance and utility by fast ex vivo and in vivo imaging of human skin. With the ability to provide rapid access to depth resolved images of skin over cm 2 area and to generate 3D distribution maps of key sub-cellular skin components such as melanocytic dendrites and melanin, FLAME represents a promising imaging tool for enhancing diagnosis accuracy, guiding therapy and understanding skin biology.
Use of GitHub as a platform for open collaboration on text documents (2015)

Recently, researchers are paying attention to the use of the software development and code-hosting web service GitHub for other collaborative purposes, including a class of activity referred to as document, text, or prose collaboration. These alternative uses of GitHub as a platform for sharing non-code artifacts represent an important modification in the practice of open collaboration. We survey cases where GitHub has been used to facilitate collaboration on non-code outputs, identify its strengths and weaknesses when used in this mode, and propose conditions for successful collaborations on co-created text documents.