gebhart/patrepeval huggingface dataset:
The 2022 Nobel Prize in Chemistry—sweet! (2023)

On 2022 October 5, The Royal Swedish Academy of Sciences announced its decision to award the Nobel Prize in Chemistry 2022 to Carolyn R. Bertozzi (Stanford University), Morten Meldal (University of Copenhagen), and K. Barry Sharpless (Scripps Research) “for the development of click chemistry and bioorthogonal chemistry.” The glycobiology community was exultant! To understand why, one must appreciate how challenges in glycoscience research motivated the development of these transformative chemical tools. Glycoscience has a storied history contributing significant discoveries to hematology, metabolism, microbiology, and other fields of biomedical research throughout much of the 20th century. But when the 1970s and 80s ushered in new molecular biology methods that accelerated studies of nucleic acid and protein function, studies of glycans began to lag behind (National Research Council 2012; Agre et al. 2016). Fortunately, since then, vast improvements have been made in areas such as carbohydrate synthesis and glycan arrays (Rillahan and Paulson 2011; Li and Bennett 2022), availability of glyco-enzymes and small molecule inhibitors (Moremen et al. 2018; Almahayni et al. 2022), mass spectrometry analysis of glycans and glycopeptides (Ruhaak et al. 2018; Suttapitugsakul et al. 2020; Bagdonaite et al. 2022), as well understanding of biological systems (Varki 2017), all of which have facilitated studies of glycan function. Notwithstanding these and other important advances, glycan detection has presented a recurrent challenge. Indeed, much of the modern practice of biological research hinges on the ability to specifically address a biomolecule of interest so that it can be isolated, visualized, or quantified. For nucleic acids, this can often be achieved via hybridization, whereas specific proteins can be detected and tracked using antibodies or protein tagging methods. But genetically encoded tags cannot be used to track glycans, which are not primary gene products. For the glycobiologist, lectins and antibodies have been essential tools but can suffer from limitations relating to specificity and affinity (Cummings et al. 2022).
A Novel Low-Loss Modulation Strategy for High-Power Bidirectional Buck ${\bm +}$ Boost Converters (2009)

A novel, low-loss, constant-frequency, zero-voltage-switching (ZVS) modulation strategy for bidirectional, cascaded, buck-boost DC-DC converters, used in hybrid electrical vehicles or fuel cell vehicles (FCVs), is presented and its benefits over state-of-the-art converters and soft-switching solutions are discussed in a comparative evaluation. To obtain ZVS with the proposed modulation strategy, the buck+boost inductance is selected and the switches are gated in a way that the inductor current has a negative offset current at the beginning and the end of each pulse period. This allows the MOSFET switches to turn on when the antiparallel body diode is conducting. As the novel modulation strategy is a software-only solution, there are no additional expenses for the active or passive components compared to conventional modulation implementations. Furthermore, an analytical and simulation investigation predicts an excellent efficiency over the complete operating range and a higher power density for a nonisolated multiphase converter equipped with the low-loss modulation. Experimental measurements performed with 12 kW, 17.4 kW/L prototypes in stand-alone and multiphase configuration verify the low-loss operation over a wide output power range and a maximum efficiency of 98.3% is achieved.
Direct Copper(III) Formation from O2 and Copper(I) with Histamine Ligation (2016)

Histamine chelation of copper(I) by a terminal histidine residue in copper hydroxylating enzymes activates dioxygen to form unknown oxidants, generally assumed as copper(II) species. The direct formation of copper(III)-containing products from the oxygenation of histamine-ligated copper(I) complexes is demonstrated here, indicating that copper(III) is a viable oxidation state in such products from both kinetic and thermodynamic perspectives. At low temperatures, both trinuclear Cu(II)2Cu(III)O2 and dinuclear Cu(III)2O2 predominate, with the distribution dependent on the histamine ligand structure and oxygenation conditions. Kinetics studies suggest the bifurcation point to these two products is an unobserved peroxide-level dimer intermediate. The hydrogen atom reactivity difference between the trinuclear and binuclear complexes at parity of histamine ligand is striking. This behavior is best attributed to the accessibility of the bridging oxide ligands to exogenous substrates rather than a difference in oxidizing abilities of the clusters.
A scattered data approximation tool to map single-walled carbon nanotube dispersion to the processing parameters in polymer nanocomposites (2010)

The relationship of nanocomposite dispersion to dispersion techniques and other processing parameters was studied. Examining all permutations of the various factors in the laboratory is a challenging task. In this paper, we propose to map a correlation between inputs and output via a self-adaptive scattered data approximation method. The proposed greedy algorithm, sequential function approximation (SFA), reveals the multidimensional behaviour of the system, provides the sensitivity of each input and presents the combination of inputs that is most suitable for a specific output. In this research, we have collected data from various research institutions and applied it to SFA. The results show that SWNT weight percent, sonication time, SWNT modification and high shear mixing time are key factors that affect the dispersion. This text discusses SFA, the data and the results in detail. This work serves as a proof of concept for functional mapping to be applied to polymer processing.
Load Balanced Sort on Hypercube Multiprocessors (2005)

A parallel algorithm for sorting n elements evenly distributed over 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sup> = p nodes of a d-dimensional hypercube is given. The algorithm ensures that the nodes always receive equal number of elements (n/p) at the end, regardless of the skew in data distribution.
Future InBodied: A Framework for Inbodied Interaction Design (2020)

Inbodied interaction is an emerging area in HCI that aligns how the body performs internally with our designs to support and optimise human performance. Inbodied Interaction therefore relies on knowledge of our physiology/neurology/kinesiology etc, to blend with HCI methodology. Recent, Inbodied Interaction workshops and summer schools, have been designed to share models of these processes to accelerate access to these areas of specialisation for HCI researchers. As such this one-day-hands-on-studio presents an extension of this work - an Inbodied interaction framework - to (1) make inbodied sciences accessible and (2) usable for HCI practitioners when it comes to crafting experiences, whether for health, performance or play. Our framework also offers a design alternative to cyborging futures that seek to augment human performance, Inbodied Interaction seeks to help discover and optimise human potential. As such, in this studio, we will explore where inbodied interaction fits in the narrative of our future bodies.
Wireless Sensing in Complex Electromagnetic Media: Construction Materials and Structural Monitoring (2015)

In this paper, wireless sensing in the presence of complex electromagnetic media created by combinations of reinforcing bars and concrete is investigated. The wireless displacement sensing system, primarily designed for use in structural health monitoring (SHM), is composed of a comb-like nested split-ring resonator (NSRR) probe and a transceiver antenna. Although each complex medium scenario is predicted to have a detrimental effect on sensing in principle, it is demonstrated that the proposed sensor geometry is able to operate fairly well in all scenarios except one. In these scenarios that mimic real-life SHM, it is shown that this sensor exhibits a high displacement resolution of 1 μm, a good sensitivity of 7 MHz/mm in average, and a high dynamic range extending over 20 mm. For the most disruptive scenario of placing concrete immediately behind NSRR, a solution based on employing a separator behind the probe is proposed to overcome the handicaps introduced by the medium. In order to obtain a one-to-one mapping from the measured frequency shift to the displacement, a numerical fit is proposed and used. The effects of several complex medium scenarios on this fit are discussed. These results indicate that the proposed sensing scheme works well in real-life SHM applications.
Medicinal peptide drugs in evidence-based medicine (2021)

Статья посвящена обзору исследований эффективности и безопасности пептидных лекарственных препаратов с точки зрения доказательной медицины. В отношении лекарственных средств доказательная медицина опирается на анализ информации, полученной в процессе оценки преимуществ и рисков при проведении клинических испытаний, в частности, рандомизированных двойных слепых плацебо-контролируемых исследований. На основании систематизированного подхода проводится мета-анализ, который представляет собой обобщение и статистический анализ результатов нескольких исследований. Обзор выполненных статистических исследований показал безусловную клиническую эффективность лекарственных пептидных препаратов The article reviews the efficacy and safety of medicinal peptide drugs from the perspective of evidence-based medicine. With regard to medicinal drugs, evidence-based medicine relies on the analysis of information obtained by assessing the benefits and risks of clinical trials and, in particular, randomized double-blind placebo-controlled trials. Based on a systematic review, a meta-analysis, which is a summary and statistical analysis of the results of multiple studies, was performed. This analysis of reported statistical studies proved the unconditional clinical efficacy of medicinal peptide drugs.
Assessment of Growth Parameters and Life Span of GHR/BP Gene-Disrupted Mice1 (2000)

GH has many biological roles, including promotion of growth. Most, if not all, of its roles are achieved through interaction with its receptor. We chose to study the effects of loss of GH signaling on growth and aging in a mouse model for Laron Syndrome (LS) in which the GHR/BP gene has been disrupted. We observed that mice homozygous for the disruption (-/-) were significantly smaller than normal wild-type (+/+) mice as well as mice heterozygous for the disruption, even at 1.5 yr of age. IGF-I levels were also significantly lower in the -/- mice and remained low as the mice aged. IGFBP-3 levels were severely reduced in the -/- mice, whereas IGFBP-1, -2, and -4 levels remained unchanged. Finally, the -/- mice lived significantly longer than +/+ and +/- mice. The latter result contradicts the anti-aging GH data and suggests the need for further analysis of GH and aging.
Mouse Genetic Background Is a Major Determinant of Isotype-Related Differences for Antibody-Mediated Protective Efficacy against Cryptococcus neoformans (2005)

The protective efficacy of mAbs to Cryptococcus neoformans glucuronoxylomannan depends on Ab isotype. Previous studies in A/JCr and C57BL/6J mice showed relative protective efficacy of IgG1, IgG2a >> IgG3. However, we now report that in C57BL/6J x 129/Sv mice, IgG3 is protective while IgG1 is not protective, with neither isotype being protective in 129/Sv mice. IgG1, IgG2a, and IgG3 had different effects on IFN-gamma expression in infected C57BL/6J x 129/Sv mice. IgG1-treated C57BL/6J x 129/Sv mice had significantly more pulmonary eosinophilia than IgG2a- and IgG3-treated C57BL/6J x 129/Sv mice. C. neoformans infection and Ab administration had different effects on FcgammaRI, FcgammaRII, and FcgammaRIII expression in C57BL/6J, 129/Sv, and C57BL/6J x 129/Sv mice. Our results indicate that the relative efficacy of Ab isotype function against C. neoformans is a function of the genetic background of the host and that IgG3-mediated protection in C57BL/6J x 129/Sv mice was associated with lower levels of IFN-gamma and fewer pulmonary eosinophils. The dependence of isotype efficacy on host genetics underscores a previously unsuspected complex relationship between the cellular and humoral arms of the adaptive immune response.
Genome-Wide Prediction of C. elegans Genetic Interactions (2006)

To obtain a global view of functional interactions among genes in a metazoan genome, we computationally integrated interactome data, gene expression data, phenotype data, and functional annotation data from three model organisms-Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster-and predicted genome-wide genetic interactions in C. elegans. The resulting genetic interaction network (consisting of 18,183 interactions) provides a framework for system-level understanding of gene functions. We experimentally tested the predicted interactions for two human disease-related genes and identified 14 new modifiers.
Abstract P3-02-06: Tracing glucose catabolism in human triple negative breast cancer tumors (2020)

Abstract Triple negative breast cancer (TNBC) is an aggressive tumor type for which few targeted treatments exist. Altered tumor metabolism may provide novel diagnostic and therapeutic opportunities. Recent genetic analyses in TNBC demonstrate augmented expression of pathways related to glucose metabolism, including glycolysis, the pentose phosphate (PPP), and serine biosynthetic pathways. No studies, however, have directly probed how glucose is utilized by TNBCs in vivo. Here, we trace these metabolic fates by infusing TNBC patients with isotopically labeled 1,2-13C-glucose, a tracer that can determine which of these pathways predominate. Upon achieving stable tracer enrichment in serum, patient primary TNBC biopsies were collected and flash frozen. Subsequent analysis by liquid chromatography mass spectroscopy (LC-MS) revealed most TNBC tumors locally ferment glucose to lactate, with limited exchange of pyruvate/lactate with the systemic circulation. This contrasts with lung cancer, where pyruvate/lactate exchange is extensive. In addition, isotopic labeling patterns indicate that glycolysis dominates the PPP in terms of total flux. Nevertheless, ribose-phosphate for nucleotide synthesis consistently arises from the oxidative branch of the PPP. Furthermore, a subset of patients demonstrated high levels of de novo serine production. To better understand these observations, next generation sequencing (NGS) and reverse phase protein array (RPPA) analyses on adjacent biopsies from these patients are underway. Together, these findings provide the first comprehensive in vivo characterization of glucose metabolism in TNBC and raise the potential to use tracing to guide development of metabolic therapeutics. Citation Format: Jonathan Michael Ghergurovich, Joyce O’Shaughnessy, Maren K Levin, Aaron Killian, William Hendricks, Virginia Espina, Joshua D Rabinowitz. Tracing glucose catabolism in human triple negative breast cancer tumors [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-02-06.
Triethylborane and methyl vinyl ketone as a bicom-ponent transfer agent for the polymerisation of styrene (2000)

The polymerisation of styrene in the presence of methyl vinyl ketone (MVK) and triethylborane (BEt3)was studied. The mixture of these two compounds was found to form a bicomponent complex that functions as a transfer agent for growing polystyryl radicals (CT = 0.7; benzene, 60 °C). The analysis of the polymer chains formed by MALDI-TOF-MS showed that they were fitted with CH2—CH3 and CH2—CH2—C(O)—CH3 as end groups which obviously emanated from MVK and BEt3. In contrast, no such transfer occurred on using each of them as single compound.
Current practice and novel approaches in organ preservation (2023)

Organ transplantation remains the only treatment option for patients with end-stage organ failure. The last decade has seen a flurry of activity in improving organ preservation technologies, which promise to increase utilization in a dramatic fashion. They also bring the promise of extending the preservation duration significantly, which opens the doors to sharing organs across local and international boundaries and transforms the field. In this work, we review the recent literature on machine perfusion of livers across various protocols in development and clinical use, in the context of extending the preservation duration. We then review the next generation of technologies that have the potential to further extend the limits and open the door to banking organs, including supercooling, partial freezing, and nanowarming, and outline the opportunities arising in the field for researchers in the short and long term.
Photoacoustic measurement of methane concentrations with a compact pulsed optical parametric oscillator (2002)

A pulsed periodically poled lithium niobate optical parametric oscillator operating in a cavity with a grazing-incidence grating configuration was used for sensitive and precise measurement of trace quantities of methane in nitrogen by photoacoustic spectroscopy with a novel differential photoacoustic detector. A sensitivity of 1.2 parts in 10(9) by volume of methane was obtained in direct calibration measurements (not extrapolated). With this apparatus, in situ measurement of the methane concentration in ambient air under atmospheric conditions was demonstrated.
Expert Panel on Weight Loss Surgery: Executive Report Update (2009)

Rapid shifts in the demographics and techniques of weight loss surgery (WLS) have led to new issues, new data, new concerns, and new challenges. In 2004, this journal published comprehensive evidence-based guidelines on WLS. In this issue, we've updated those guidelines to assure patient safety in this fast-changing field. WLS involves a uniquely vulnerable population in need of specialized resources and ongoing multidisciplinary care. Timely best-practice updates are required to identify new risks, develop strategies to address them, and optimize treatment. Findings in these reports are based on a comprehensive review of the most current literature on WLS; they directly link patient safety to methods for setting evidence-based guidelines developed from peer-reviewed scientific publications. Among other outcomes, these reports show that WLS reduces chronic disease risk factors, improves health, and confers a survival benefit on those who undergo it. The literature also shows that laparoscopy has displaced open surgery as the predominant approach; that government agencies and insurers only reimburse procedures performed at accredited WLS centers; that best practice care requires close collaboration between members of a multidisciplinary team; and that new and existing facilities require wide-ranging changes to accommodate growing numbers of severely obese patients. More than 100 specialists from across the state of Massachusetts and across the many disciplines involved in WLS came together to develop these new standards. We expect them to have far-reaching effects of the development of health care policy and the practice of WLS.
Threshold properties of a microcavity laser with submicroampere threshold current (1996)

We report the threshold characteristics of small oxide-confined vertical-cavity surface emitting lasers. Abrupt threshold transitions 105 times the spontaneous emission background are obtained at injection currents as low as 470 nanoampere.
Mental Health Symptom Reduction Using Digital Therapeutics Care Informed by Genomic SNPs and Gut Microbiome Signatures (2022)

Neuropsychiatric diseases and obesity are major components of morbidity and health care costs, with genetic, lifestyle, and gut microbiome factors linked to their etiology. Dietary and weight-loss interventions can help improve mental health, but there is conflicting evidence regarding their efficacy; and moreover, there is substantial interindividual heterogeneity that needs to be understood. We aimed to identify genetic and gut microbiome factors that explain interindividual differences in mental health improvement after a dietary and lifestyle intervention for weight loss. We recruited 369 individuals participating in Digbi Health’s personalized digital therapeutics care program and evaluated the association of 23 genetic scores, the abundance of 178 gut microbial genera, and 42 bacterial pathways with mental health. We studied the presence/absence of anxiety or depression, or sleep problems at baseline and improvement on anxiety, depression, and insomnia after losing at least 2% body weight. Participants lost on average 5.4% body weight and >95% reported improving mental health symptom intensity. There were statistically significant correlations between: (a) genetic scores with anxiety or depression at baseline, gut microbial functions with sleep problems at baseline, and (b) genetic scores and gut microbial taxa and functions with anxiety, depression, and insomnia improvement. Our results are concordant with previous findings, including the association between anxiety or depression at baseline with genetic scores for alcohol use disorder and major depressive disorder. As well, our results uncovered new associations in line with previous epidemiological literature. As evident from previous literature, we also observed associations of gut microbial signatures with mental health including short-chain fatty acids and bacterial neurotoxic metabolites specifically with depression. Our results also show that microbiome and genetic factors explain self-reported mental health status and improvement better than demographic variables independently. The genetic and microbiome factors identified in this study provide the basis for designing and personalizing dietary interventions to improve mental health.
Space-charge limited current in regioregular poly-3-hexyl-thiophene (2003)

Temperature dependent current–voltage characteristics of an organic diode based on a thin film of regioregular poly-3-hexyl-thiophene (P3HT) are compared with results of a theoretical model assuming space-charge limited currents with a density of states (DOS), nonmonotonous in energy. This DOS was deduced from experiments utilizing the method of thermally stimulated currents. Both, experiments and theory result in an almost power-law dependence of j∝Vm, where the exponent m increases with decreasing temperature assuming a value of m=2 at room temperature. This effect can be accounted for by filling of deep traps at lower temperatures. Transport of charge carriers in P3HT seems to be limited by hopping in disordered regions rather than by the transport via extended states within crystalline grains.