gebhart/patrepeval huggingface dataset:
Molecular Analysis of Shower Curtain Biofilm Microbes (2004)

Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as "soap scum," which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the alpha-group of proteobacteria, mainly Sphingomonas spp. and Methylobacterium spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.
Nucleotides and Two Functional States of hsp90 (1997)

Previous studies have demonstrated the ATP-dependent formation of a complex containing the heat shock protein hsp90, the unique hsp90 binding protein p23, and one of three high molecular weight immunophilins. In the present study, hsp90 and p23 are shown to form a complex that requires elevated temperature and ATP/Mg2+. Complex formation is strongly promoted by molybdate and by the nonionic detergent Nonidet P-40. ADP and the benzoquinone ansamycin, geldanamycin, are potent inhibitors of complex formation. The ATP-dependent process alters the state of hsp90, not p23, and influences the ability of hsp90 to bind to phenyl-Sepharose. Conversion of hsp90 to the ATP-bound state lowers its affinity for phenyl-Sepharose. These results show that hsp90 can exist in at least two functional states, one able to bind p23 and the other with a high affinity for hydrophobic resins. A model is presented where these states are dictated by the binding of either ATP or ADP.
Semantic Function as a Mathematical Model of Quantum Conceptualism (2025)

Since its inception, many physicists have seen in quantum mechanics the possibility, if not the necessity, of bringing cognitive aspects into the play, which were instead absent, or unnoticed, in the previous classical theories. In this article, we outline the path that led us to support the hypothesis that our physical reality is fundamentally conceptual-like and cognitivistic-like. However, contrary to the “abstract ego hypothesis” introduced by John von Neumann and further explored, in more recent times, by Henry Stapp, our approach does not rely on the measurement problem as expressing a possible “gap in physical causation,” which would point to a reality lying beyond the mind-matter distinction. On the contrary, in our approach, the measurement problem is considered to be essentially solved, at least for what concerns the origin of quantum probabilities, which we have reasons to believe they would be epistemic. Our conclusion that conceptuality and cognition would be an integral part of all physical processes comes instead from the observation of the striking similarities between the non-spatial behavior of the quantum micro-physical entities and that of the human concepts. This gave birth to a new interpretation of quantum mechanics, called the “conceptuality interpretation,” currently under investigation within our group in Brussels.
Tandem Mass Spectrometric Analysis of Dried Blood Spots for Screening of Mucopolysaccharidosis I in Newborns (2005)

Mucopolysaccharidosis type I (MPS-I), caused by a deficiency of α-l-iduronidase (IDUA; EC 3.2.1.76) activity, can manifest as three major phenotypes, usually defined by clinical criteria: Hurler (severe), Scheie (mild), and Hurler–Scheie (intermediate) syndromes.

IDUA is crucial for degradation of glycosaminoglycans such as dermatan and heparan sulfate. Failure to break down these polysaccharides causes physical changes such as joint stiffness, skeletal abnormalities, and corneal clouding. Hurler syndrome is characterized by valvular heart disease, mental deterioration, and death in childhood. Enzyme replacement therapy has been developed for MPS-I, and bone marrow transplantation is beneficial if performed early (1). Because early detection is necessary for optimum clinical response to therapy, the need for newborn screening of MPS-I is under active discussion.

Lysosomal enzymes can be measured in rehydrated dried blood spots (DBS) (2)(3)(4)(5)(6)(7)(8). Fluorometric, radiometric, and electrospray ionization tandem mass spectrometry (ESI-MS/MS) assays have been developed. The latter offer the capability of assaying the products of several enzymes simultaneously (multiplexing) (8). In this report, we describe an ESI-MS/MS assay that directly measures the reaction velocity of IDUA in rehydrated DBS for the newborn screening of MPS-I. We also show that the assay can be combined with ESI-MS/MS assays of Niemann–Pick type A/B, Krabbe, Gaucher, Pompe, and Fabry diseases (8) for the simultaneous analysis of six lysosomal storage diseases.

All experiments with DBS were conducted in compliance with Institutional Review Board review. All MPS-I-affected patients had been diagnosed previously with established clinical and biochemical procedures. DBS were kept at ambient temperature during shipment (<10 days) and then stored at −20 °C in zip-lock plastic bags (one bag sealed inside of a second bag). Zip-lock bags were kept in a sealed plastic box containing desiccant (anhydrous CaSO4 granules). We developed …
Genome-Editing Technologies: Concept, Pros, and Cons of Various Genome-Editing Techniques and Bioethical Concerns for Clinical Application (2019)

The traditional healthcare system is at the doorstep for entering into the arena of molecular medicine. The enormous knowledge and ongoing research have now been able to demonstrate methodologies that can alter DNA coding. The techniques used to edit or change the genome evolved from the earlier attempts like nuclease technologies, homing endonucleases, and certain chemical methods. Molecular techniques like meganuclease, transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs) initially emerged as genome-editing technologies. These initial technologies suffer from lower specificity due to their off-targets side effects. Moreover, from biotechnology's perspective, the main obstacle was to develop simple but effective delivery methods for host cell entry. Later, small RNAs, including microRNA (miRNA) and small interfering RNA (siRNA), have been widely adopted in the research laboratories to replace lab animals and cell lines. The latest discovery of CRISPR/Cas9 technology seems more encouraging by providing better efficiency, feasibility, and multi-role clinical application. This later biotechnology seem to take genome-engineering techniques to the next level of molecular engineering. This review generally discusses the various gene-editing technologies in terms of the mechanisms of action, advantages, and side effects.
A receiver of simple structure for antenna array CDMA systems (1999)

In code division multiple access systems, the two-dimensional (2-D) RAKE structure had been proposed using multiple antennas to increase the capacity. It consists of multiple fingers of a beamformer and a correlator. In this paper, we consider a simpler receiver structure. We only use one finger, which consists of one pair of spatial and temporal filters to combine signals. It is shown that the performance of the receiver system is comparable with that of the 2-D RAKE receiver. Furthermore, it is observed that the proposed receiver and the 2-D RAKE receiver have limited near-far resistance by the generation of the space domain due to antenna arrays.
Lipid-Based Signaling Modulates DNA Repair Response and Survival against <i>Klebsiella pneumoniae</i> Infection in Host Cells and in Mice (2013)

Klebsiella pneumoniae causes serious infections in the urinary tract, respiratory tract, and blood. Lipid rafts, also known as membrane microdomains, have been linked to the pathogenesis of bacterial infection. However, whether lipid rafts affect K. pneumoniae internalization into host cells remains unknown. Here, we show for the first time that K. pneumoniae was internalized into lung cells by activating lipid rafts. Disrupting lipid rafts by methyl-β-cyclodextrin inhibited pathogen internalization, impairing host defense. A deficient mutant of capsule polysaccharide (CPS) showed a higher internalization rate than a wild-type strain, indicating that CPS may inhibit bacterial entry to host cells. Furthermore, lipid rafts may affect the function of extracellular regulated kinase (ERK)-1/2, and knocking down ERK1/2 via short, interfering RNA increased apoptosis in both alveolar macrophages and epithelial cells after infection. To gain insights into bacterial pathogenesis, we evaluated the impact of lipid rafts on DNA integrity, and showed that raft aggregates also affect DNA damage and DNA repair responses (i.e., 8-oxoguanine DNA glycosylase [Ogg1]) through the regulation of reactive oxygen species. Importantly, cells overexpressing Ogg1 demonstrated reduced cytotoxicity during bacterial infection. Taken together, these results suggest that lipid rafts may modulate bacterial internalization, thereby affecting DNA damage and repair, which is critical to host defense against K. pneumoniae.
Wet oxidation efficiencies of perchloric acid mixtures for various organic substances and the identities of residual matter (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTWet oxidation efficiencies of perchloric acid mixtures for various organic substances and the identities of residual matterGary D. Martinie and Alfred A. SchiltCite this: Anal. Chem. 1976, 48, 1, 70–74Publication Date (Print):January 1, 1976Publication History Published online1 May 2002Published inissue 1 January 1976https://pubs.acs.org/doi/10.1021/ac60365a032https://doi.org/10.1021/ac60365a032research-articleACS PublicationsRequest reuse permissionsArticle Views265Altmetric-Citations97LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Light-induced performance increase of silicon heterojunction solar cells (2016)

Silicon heterojunction solar cells consist of crystalline silicon (c-Si) wafers coated with doped/intrinsic hydrogenated amorphous silicon (a-Si:H) bilayers for passivating-contact formation. Here, we unambiguously demonstrate that carrier injection either due to light soaking or (dark) forward-voltage bias increases the open circuit voltage and fill factor of finished cells, leading to a conversion efficiency gain of up to 0.3% absolute. This phenomenon contrasts markedly with the light-induced degradation known for thin-film a-Si:H solar cells. We associate our performance gain with an increase in surface passivation, which we find is specific to doped a-Si:H/c-Si structures. Our experiments suggest that this improvement originates from a reduced density of recombination-active interface states. To understand the time dependence of the observed phenomena, a kinetic model is presented.
T Cell Dynamics and the Response to HAART in a Cohort of HIV‐1–Infected Elite Suppressors (2009)

Elite controllers or suppressors are untreated human immunodeficiency virus type 1 (HIV-1)-infected patients who maintain undetectable viral loads. In this study, we show that most elite suppressors do not experience significant changes in T cell counts over a 10-year period. Interestingly, treatment of an elite suppressor with highly active antiretroviral therapy (HAART) led to a marked decrease in immune activation.
Does the patient's position influence the detection of detrusor overactivity? (2007)

This review confirms that the patient's position is a significant variable during urodynamics and that supine cystometry will fail to detect a significant percentage of patients with DO. We suggest that all patients should be filled sitting or standing, unless physically disabled. It seems desirable for the International Continence Society (ICS) to extend its "Good urodynamic practice guideline" [Schafer et al., Neurourol Urodyn 21:261-74, 2002] to cover this important issue.
Unsupervised Visual Representation Learning via Dual-Level Progressive Similar Instance Selection (2021)

The superiority of deeply learned representations relies on large-scale labeled datasets. However, annotating data are usually expensive or even infeasible in some scenarios. To address this problem, we propose an unsupervised method to leverage instance discrimination and similarity for deep visual representation learning. The method is based on an observation that convolutional neural networks (CNNs) can learn a meaningful visual representation with instancewise classification, in which each instance is treated as an individual class. By this instancewise discriminative learning, instances can reasonably distribute in the representation space, which reveals their similarities. In order to further improve visual representations, we propose a dual-level progressive similar instance selection (DPSIS) method to build a bridge from instance to class by selecting similar instances (neighbors) for each instance (anchor) and treating the anchor and its neighbors as the same class. To be specific, DPSIS adaptively selects two levels of neighbors, that is: 1) an "absolutely similar level" and 2) a "relatively similar level." Instances in the absolutely similar level are used as hard labels, while instances in the relatively similar level are used as soft labels. Moreover, during training, DPSIS is able to progressively select more neighbors without human supervision. At the beginning of training, because CNNs are weak, most instances are distributed relatively randomly in the representation space and only a few easy-to-recognize instances are selected as neighbors. As CNN models become stronger, the semantic meaning of each instance grows clearer. Those instances originally distributed in a relatively random manner gradually move to meaningful positions. This consequently facilitates CNN training since the number of reliable samples increases. Experiments on seven benchmarks, including three small-scale and two large-scale coarse-grained image classification datasets, and two fine-grained categorization datasets, demonstrate the effectiveness of our DPSIS. Our codes have been released at https://github.com/hehefan/DPSIS.
Surface current reduction in (211) oriented Cd0.46Zn0.04Te.50 crystals by Ar bombardment (2010)

Cd 0.46 Zn 0.04 Te .50 crystals have been exposed to high density Ar plasmas in order to modify the surface chemistry and control the surface conductivity. X-ray photoelectron spectroscopy reveals that this bombardment results in a modified surface atomic ratio, with Cd being preferentially removed compared to Te. In addition, the native oxide is removed and suppressed for an extended period of time. Current-voltage data is analyzed in order to determine the effect on surface leakage current after exposure. It is found that surface leakage current can be decreased by approximately 2.5 orders of magnitude following Ar+ bombardment.
PROTECTION OF THE D1 PHOTOSYSTEM II REACTION CENTER PROTEIN FROM DEGRADATION IN ULTRAVIOLET RADIATION FOLLOWING ADAPTATION OF Brassica napus L. TO GROWTH IN ULTRAVIOLET‐B (1993)

Abstract As depletion of the stratospheric ozone layer continues, the biosphere will most likely be exposed to higher levels of ultraviolet‐B (UV‐B) irradiation (290–320nm). For plants, damage from UV‐B can occur at several molecular targets with the photosynthetic apparatus being especially vulnerable. We are interested both in the mechanisms of UV‐B‐induced damage and identifying adaptation processes that can confer protection from UV‐B. Toward this end, Brassica napus (oil seed rape) plants grown under visible light plus a low level of UV‐B radiation (adapted plants) were compared to plants grown under visible light alone (control plants). Relative to the control plants, the adapted plants showed little evidence of damage at the levels of morphology or photosynthesis, indicating that B. napus has some tolerance of UV‐B and that the plants may have protection mechanisms. Consistent with this, a strong UV‐B adaptation process was observed in the plants‐accumulation of flavonoids in the epidermis. These pigments seemed to screen a molecular target in the mesophyll. Namely, the D1 photosystem II reaction center protein, which is rapidly degraded in UV‐B, was partially protected from degradation in UV‐B in the adapted plants. Moreover, the extent that the half‐life of the D1 protein increased in the adapted plants was on par with the elevation in total flavonoid concentrations. These experiments demonstrate that degradation of the D1 protein can be used as an in vivo assay of penetration of UV‐B photons to the mesophyll.
Highly Enantioselective Intramolecular Cyclopropanation Reactions of <i>N</i>-Allylic-<i>N</i>-methyldiazoacetamides Catalyzed by Chiral Dirhodium(II) Carboxamidates (1996)

Catalytic diazo decomposition of representative N-allylic-N-methyldiazoacetamides produced the corresponding intramolecular cyclopropanation products in good to excellent yields and with exceptional enantiocontrol. In the simplest case, with N-allyl-N-methyldiazoacetamide, catalysis by dirhodium(II) tetrakis[methyl 2-oxapyrrolidine-5(S)-carboxylate], Rh2(5(S)-MEPY)4, achieved the highest yield and enantioselectivity (93% ee). Dirhodium(II) tetrakis[methyl 2-oxo-1-(3-phenylpropanoyl)imidazolidin-4(S)-carboxylate], Rh2(4S)-MPPIM)4, was preferred for substituted N-allylic-N-methyldiazoacetamides from which 92−95% ee's were obtained in intramolecular cyclopropanation reactions (88−95% yields), even when the catalyst was employed in only 0.1 mol %. Competition with intramolecular dipolar cycloaddition was minimized with the use of N-methyldiazoacetamides relative to N-tert-butyldiazoacetamides.
Successful radioimmunotherapy of established syngeneic rat colon carcinoma with 211At-mAb (2013)

This study demonstrates the possibility of treating small, solid colon carcinoma tumors with α-emitting radionuclides such as 211At bound to mAbs, with tolerable toxicity.
Localization of nuclear subunits of cyclic AMP-dependent protein kinase by the immunocolloidal gold method. (1985)

An immunocolloidal gold electron microscopy method is described allowing the ultrastructural localization and quantitation of the regulatory subunits RI and RII and the catalytic subunit C of cAMP-dependent protein kinase. Using a postembedding indirect immunogold labeling procedure that employs specific antisera, the catalytic and regulatory subunits were localized in electron-dense regions of the nucleus and in cytoplasmic areas with a minimum of nonspecific staining. Antigenic domains were localized in regions of the heterochromatin, nucleolus, interchromatin granules, and in the endoplasmic reticulum of different cell types, such as rat hepatocytes, ovarian granulosa cells, and spermatogonia, as well as cultured H4IIE hepatoma cells. Morphometric quantitation of the relative staining density of nuclear antigens indicated a marked modulation of the number of subunits per unit area under various physiologic conditions. For instance, following partial hepatectomy in rats, the staining density of the nuclear RI and C subunits was markedly increased 16 h after surgery. Glucagon treatment of rats increased the staining density of only the nuclear catalytic subunit. Dibutyryl cAMP treatment of H4IIE hepatoma cells led to a marked increase in the nuclear staining density of all three subunits of cAMP-dependent protein kinase. These studies demonstrate that specific antisera against cAMP-dependent protein kinase subunits may be used in combination with immunogold electron microscopy to identify the ultrastructural location of the subunits and to provide a semi-quantitative estimate of their relative cellular density.
SIRT1 and NRF2 Gene Transfer Mediate Distinct Neuroprotective Effects Upon Retinal Ganglion Cell Survival and Function in Experimental Optic Neuritis (2018)

AAV-mediated overexpression of NRF2 or SIRT1 within RGCs mediates distinct neuroprotective effects upon visual function and RGC survival. This study expands our understanding of SIRT1 and NRF2-mediated neuroprotection in the context of MS pathogenesis and optic neuropathies.
Flexible thin-film black gold membranes with ultrabroadband plasmonic nanofocusing for efficient solar vapour generation (2015)

Solar steam generation has been achieved by surface plasmon heating with metallic nanoshells or nanoparticles, which have inherently narrow absorption bandwidth. For efficient light-to-heat conversion from a wider solar spectrum, we employ adiabatic plasmonic nanofocusing to attain both polarization-independent ultrabroadband light absorption and high plasmon dissipation loss. Here we demonstrate large area, flexible thin-film black gold membranes, which have multiscale structures of varying metallic nanoscale gaps (0-200 nm) as well as microscale funnel structures. The adiabatic nanofocusing of self-aggregated metallic nanowire bundle arrays produces average absorption of 91% at 400-2,500 nm and the microscale funnel structures lead to average reflection of 7% at 2.5-17 μm. This membrane allows heat localization within the few micrometre-thick layer and continuous water provision through micropores. We efficiently generate water vapour with solar thermal conversion efficiency up to 57% at 20 kW m(-2). This new structure has a variety of applications in solar energy harvesting, thermoplasmonics and related technologies.