gebhart/patrepeval huggingface dataset:
Emerging Chemistry Strategies for Engineering Native Chromatin (2017)

Chromosomes present one of most challenging of all substrates for biochemical study. This is because genomic DNA is physically associated with an astonishing collection of nuclear factors, which serve to not only store the nucleic acid in a stable form, but also grant access to the information it encodes when needed. Understanding this complex molecular choreography is central to the field of epigenetics. One of the great challenges in this area is to move beyond correlative type information, which is now in abundant supply, to the point where we can truly connect the dots at the molecular level. Establishing such causal relationships requires precise manipulation of the covalent structure of chromatin. Tools for this purpose are currently in short supply, creating an opportunity that, as we will argue in this Perspective, is well suited to the sensibilities of the chemist.
Optimal Detection for One-Shot Transmission Over Diffusion-Based Molecular Timing Channels (2018)

This paper studies optimal detection for communication over diffusion-based molecular timing (DBMT) channels. The transmitter simultaneously releases multiple information particles, where the information is encoded in the time of release. The receiver decodes the transmitted information based on the random time of arrival of the information particles, which is modeled as an additive noise channel. For a DBMT channel without flow, this noise follows the Lévy distribution. Under this channel model, the maximum-likelihood (ML) detector is derived and shown to have high computational complexity. It is also shown that under ML detection, releasing multiple particles improves performance, while for any additive channel with α-stable noise where α <; 1 (such as the DBMT channel), under linear processing at the receiver, releasing multiple particles degrades performance relative to releasing a single particle. Hence, a new low-complexity detector, which is based on the first arrival (FA) among all the transmitted particles, is proposed. It is shown that for a small number of released particles, the performance of the FA detector is very close to that of the ML detector. On the other hand, error exponent analysis shows that the performance of the two detectors differ when the number of released particles is large.
SAS Sveriges förändringsarbete - förankring hos medarbetarna (2008)

Syftet med vårt arbete var att utvärdera om Scandinavian Airlines Sverige har förankrat de pågående förändringarna i organisationen hos sina medarbetare. Vi har analyserat hur Scandinavian Airlines Sverige arbetar med att motivera medarbetarna och förändra värderingar och normer bland dem. Vi har utgått ifrån Strategi 2011 och belyst den del som berör medarbetarperspektivet av den kulturella turnaround som sker inom SAS koncernen. I vår undersökning har vi avgränsat oss till Scandinavian Airlines Sverige och utgår ifrån deras tolkning av strategin som de benämner ”Framtidsresan”. Den teoretiska modellen som utarbetats har givit oss möjlighet att analysera förändringsarbetet för Scandinavian Airlines Sverige och utvärdera hur förändringarna påverkar organisationens medarbetare. Den utgår ifrån variablerna Kommunikation, Förändringsarbetet, Medarbetarnas förhållningssätt och Medarbetarnas förutsättningar. De slutsatser som vi kommit fram till är att Scandinavian Airlines Sveriges interna kommunikation till stor del har varit en ensidig och formell kommunikation från företagets sida. Medarbetarna har inte i någon större utsträckning fått vara aktiva i en dialog. Förankringen av förändringsarbetet har påverkats av att informationen inte fullt ut behandlat vad som ska ske med medarbetaren eller på arbetsplatsen. Vi anser att förankringen av förändringen förbättras om Scandinavian Airlines Sverige kunde ha involverat fler personer från organisationen än de 40 underchefer som skedde när de utvecklade ”Framtidsresan” med dess vision och strategier. Det skulle öka möjligheten till dialog med medarbetarna och utjämna kulturella skillnader samt generera ett bättre framtida resultat med förändringsarbetet. Ett annat sätt är att arbeta med förändring i mindre grupper där medarbetarna kan känna sig mer delaktiga och bättre föra en dialog. Genom att öppna för dialog och delaktighet i mindre grupper, ge feedback och samverka mer är flera sätt att förbättra motivationen. Det anser vi vara en nödvändighet för att lyckas med den stora kulturella förändringen.
Multiplexed mass spectometic quantitation of HER1-3, cMET, and IGF1R in FFPE tumor samples: Implications for targeted therapy and resistance. (2012)

e21068 Background: The human EGF receptor family (HER’s) consists of two clinically validated drug targets (EGFR and HER2), and two receptors (HER3 and HER4) which are the subject of intensive preclinical and early clinical investigation. Although drugs inhibiting both EGFR and HER2 show significant antitumor activity in the clinic, the acquisition of resistance is a hallmark of these and other targeted therapies. In the case of both targets, one of the emerging resistance mechanisms is the co-expression of other receptor tyrosine kinases, including members of the EGFR superfamily, cMet and IGF1R. As an example, it was recently shown that HER2 co-expression mediates resistance in cetuximab treated head and neck cancer. Similarly, much attention has been paid to HER3 both as a bona fide drug target and a resistance mechanism. Methods: Using trypsin digestion mapping of recombinant proteins, we identified unique peptide sequences from each of these receptors, and built quantitative mass spectrometric (MS) assays which could be multiplexed into a single MS analysis of 1ug of tumor protein. Assays were preclinically validated on 10 formalin fixed cell lines, and FFPE human NSCLC primary tumor xenografts. Results: The validated multiplex assay was used to measure expression levels of HER1-3, cMET and IGF1R in two cohorts of clinical tumor tissue which had been treated with HER family antagonists. One, a set of gefitinib treated NSCLC tumors (N=15) , and a second, a cohort of advanced breast cancer tissues which had adjuvant treatment with trastuzumab(N=18). Here we present expression patterns for each of the RTKs studied, with the intent to begin to define the relationship between RTK expression and response to either gefitinib or trastuzumab treatment. Conclusions: It is important to not only understand primary mechanisms of tumor growth, but also mechanisms of resistance in patients undergoing targeted therapies. Our Liquid Tissue-SRM promises to be a platform which can deliver extremely high sensitivity, absolute specificity as well as multiplexing capabilities to assess critical oncology targets.
Visual-Vestibular Habituation and Balance Training for Motion Sickness (1999)

Abstract Background and Purpose. This case report describes physical therapy for motion sickness in a 34-year-old woman. The purpose of the report is twofold: (1) to provide an overview of the literature regarding motion sickness syndrome, causal factors, and rationale for treatment and (2) to describe the evaluation and treatment of a patient with motion sickness. Case Description and Outcomes. The patient initially had moderate to severe visually induced motion sickness, which affected her functional abilities and prevented her from working. Following 10 weeks of a primarily home-based program of visual-vestibular habituation and balance training, her symptoms were alleviated and she could resume all work-related activities. Discussion. Although motion sickness affects nearly one third of all people who travel by land, sea, or air, little documentation exists regarding prevention or management.
NRL materials testing facility (2012)

The Naval Research Laboratory performs basic research on high power railgun electric launchers. The program uses a 1.5-MJ, 2.5 km/s launch velocity railgun located in NRL's Materials Testing Facility. The railgun consists of an 11-MJ capacitive energy store configured as 22, 0.5-MJ modules. Each bank module has an independently triggered thyristor switch, series inductor, and crowbar diode and is joined to the railgun breech with coaxial cables. Individual bank timing and charge levels can be set to produce up to 1.5 MA peak current and 4-5 ms long current pulses. The 6-m long railgun used a nominally 5 cm bore diameter with steel or copper rails and epoxy laminate insulators. The muzzle contains a Tungsten-Copper arc horn to minimize damage from residual drive current upon launch. Aluminum armatures with acrylic bore riders are used for the launch package. Launch data is recorded digitally and analyzed using in-house computer codes. The system design and operation will be discussed.
High-dose exogenous iron following cecal ligation and puncture increases mortality rate in mice and is associated with an increase in gut epithelial and splenic apoptosis* (2004)

High-dose iron supplementation with iron dextran after the onset of sepsis significantly increases mortality rate in this animal model. Iron-induced mortality may be mediated by an increase in gut epithelial and splenic apoptosis, whereas severity of bacteremia does not appear to play a causative role.
Viral load quantitation at the point-of-care with shaken digital droplet RT-LAMP (2023)

Viral load quantitation is useful in clinical point-of-care settings to assess the status of patients with infectious disease, track response to treatment, and estimate infectiousness. However, existing methods for quantitating viral loads are complex and difficult to integrate into these settings. Here, we describe a simple, instrument-free approach for viral load quantitation suitable for point-of-care use. We develop a shaken digital droplet assay that can quantitate SARS-CoV2 with sensitivity comparable to gold standard qPCR.
O apoio psicossocial e as vivências acadêmicas dos estudantes universitários (2022)

Introdução: A população universitária tem, cada vez mais, buscado suportes para enfrentar as dificuldades psicossociais vivenciadas no Ensino Superior. As vivências acadêmicas; o adoecimento mental; as condições socioeconômicas e educacionais; e a presente pandemia da COVID-19 podem alterar as percepções de segurança, conforto e pertencimento do estudante à universidade. É importante que essas instituições possibilitem os discentes a vivenciarem essa fase de forma mais adaptativa, a fim de evitar o surgimento de distúrbios mentais e desigualdades socioeconômicas. Objetivo: Nesse estudo, foi analisado as contribuições da atenção psicossocial nas vivências acadêmicas dos universitários. Método: Trata-se de estudo qualitativo, no qual foi realizado um levantamento bibliográfico de pesquisas e legislações brasileiras que envolvem a assistência estudantil; o apoio psicossocial; e as vivências acadêmicas. Resultados: Os serviços institucionais de apoio podem promover o empoderamento do estudante frente as suas adversidades. Para isso, entende-se a necessidade de identificar dados como: o perfil do estudante de cada instituição, em todos os níveis de ensino; o perfil do estudante usuário da assistência estudantil; o perfil de saúde desses estudantes; quais modelos de atenção à saúde existem na assistência estudantil; ações e estratégias para enfrentamento dos conflitos interpessoais; o equilíbrio entre a vida acadêmica e a vida pessoal; e ações de intervenção nas vivências acadêmicas. A partir dessa identificação, a universidade deve elaborar um modelo de assistência psicossocial adequada para as necessidades para o corpo estudantil. Conclusão: A atenção psicossocial deve fortalecer o vínculo entre o aluno-instituição e promover vivências acadêmicas satisfatórias e a sua permanência na universidade.
The health and economic burden of bloodstream infections caused by antimicrobial-susceptible and non-susceptible Enterobacteriaceae and Staphylococcus aureus in European hospitals, 2010 and 2011: a multicentre retrospective cohort study (2016)

We performed a multicentre retrospective cohort study including 606,649 acute inpatient episodes at 10 European hospitals in 2010 and 2011 to estimate the impact of antimicrobial resistance on hospital mortality, excess length of stay (LOS) and cost. Bloodstream infections (BSI) caused by third-generation cephalosporin-resistant Enterobacteriaceae (3GCRE), meticillin-susceptible (MSSA) and -resistant Staphylococcus aureus (MRSA) increased the daily risk of hospital death (adjusted hazard ratio (HR) = 1.80; 95% confidence interval (CI): 1.34-2.42, HR = 1.81; 95% CI: 1.49-2.20 and HR = 2.42; 95% CI: 1.66-3.51, respectively) and prolonged LOS (9.3 days; 95% CI: 9.2-9.4, 11.5 days; 95% CI: 11.5-11.6 and 13.3 days; 95% CI: 13.2-13.4, respectively). BSI with third-generation cephalosporin-susceptible Enterobacteriaceae (3GCSE) significantly increased LOS (5.9 days; 95% CI: 5.8-5.9) but not hazard of death (1.16; 95% CI: 0.98-1.36). 3GCRE significantly increased the hazard of death (1.63; 95% CI: 1.13-2.35), excess LOS (4.9 days; 95% CI: 1.1-8.7) and cost compared with susceptible strains, whereas meticillin resistance did not. The annual cost of 3GCRE BSI was higher than of MRSA BSI. While BSI with S. aureus had greater impact on mortality, excess LOS and cost than Enterobacteriaceae per infection, the impact of antimicrobial resistance was greater for Enterobacteriaceae.
Expression Levels of RAD51 Inversely Correlate with Survival of Glioblastoma Patients (2021)

Treatment failures of glioblastoma (GBM) occur within high-dose radiation fields. We hypothesized that this is due to increased capacity for DNA damage repair in GBM. We identified 24 adult GBM patients treated with maximal safe resection followed by radiation with concurrent and adjuvant temozolomide. The mRNA from patients was quantified using NanoString Technologies' nCounter platform and compared with 12 non-neoplastic temporal lobe tissue samples as a control. Differential expression analysis identified seven DNA repair genes significantly upregulated in GBM tissues relative to controls (>4-fold difference, adjusted <i>p</i> values < 0.001). Among these seven genes, Cox proportional hazards models identified RAD51 to be associated with an increased risk of death (HR = 3.49; <i>p</i> = 0.03). Kaplan-Meier (KM) analysis showed that patients with high RAD51 expression had significantly shorter OS compared to low levels (median OS of 10.6 mo. vs 20.1 mo.; log-rank <i>p</i> = 0.03). Our findings were validated in a larger external dataset of 162 patients using publicly available gene expression data quantified by the same NanoString technology (median OS of 13.8 mo. vs. 17.4 mo; log-rank <i>p</i> = 0.006). Within this uniformly treated GBM population, RAD51, in the homologous recombination pathway, was overexpressed (vs. normal brain) and inversely correlated with OS. High RAD51 expression may be a prognostic biomarker and a therapeutic target in GBM.
Secure Client-Side ST-DM Watermark Embedding (2010)

Client-side watermark embedding systems have been proposed as a possible solution for the copyright protection in large-scale content distribution environments. In this framework, we propose a new look-up-table-based secure client-side embedding scheme properly designed for the spread transform dither modulation watermarking method. A theoretical analysis of the detector performance under the most known attack models is presented and the agreement between theoretical and experimental results verified through several simulations. The experimental results also prove that the advantages of the informed embedding technique in comparison to the spread-spectrum watermarking approach, which are well known in the classical embedding schemes, are preserved in the client-side scenario. The proposed approach permits us to successfully combine the security of client-side embedding with the robustness of informed embedding methods.
Weighted Max-Min Resource Allocation for Frequency Selective Channels (2013)

In this paper, we discuss the computation of weighted max-min rate allocation among <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> users, using joint FDM/TDM strategies under a power spectral density (PSD) mask constraint. We show that the weighted max-min solution allocates the rates according to a predetermined rate ratio defined by the weights, a fact that has considerable implications for telecommunication service providers. Furthermore, we show that the problem can be efficiently solved using a linear programming technique, where at most <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> -1 frequency bins are shared by more than one user. We also address the resource allocation problem in the mixed services scenario where certain users have the required rates, while the others have flexible rate requirements. The solution is applicable to many communication systems that are limited by a power spectral density mask constraint such as UWB. The theoretical results are followed by simulations for various allocation schemes.
Investigations on soluble starch as the depressant of hematite during flotation separation of apatite (2018)

Wrocław
TAP Mediates Import of Mycobacterium tuberculosis-Derived Peptides into Phagosomes and Facilitates Loading onto HLA-I (2013)

Processing and presentation of antigen on MHC-I class I molecules serves to present peptides derived from cytosolic proteins to CD8(+) T cells. Infection with bacteria that remain in phagosomal compartments, such as Mycobacterium tuberculosis (Mtb), provides a challenge to this immune recognition as bacterial proteins are segregated from the cytosol. Previously we identified the Mtb phagosome itself as an organelle capable of loading MHC Class I molecules with Mtb antigens. Here, we find that the TAP transporter, responsible for importing peptides into the ER for loading in Class I molecules, is both present and functional in Mtb phagosomes. Furthermore, we describe a novel peptide reagent, representing the N-terminal domain of the bovine herpes virus UL49.5 protein, which is capable of specifically inhibiting the lumenal face of TAP. Together, these results provide insight into the mechanism by which peptides from intra-phagosomal pathogens are loaded onto Class I molecules.
Taming Super Lewis Acids for Catalysis: The Family of Ferrocene-Stabilized Silicon Cations (2014)

Tricoordinate silicon cations are exceptionally strong electron pair acceptors, so strong that they react with almost any σ and π basic molecule. In order to use such reactive intermediates in synthetic chemistry, Lewis acid catalysis in particular, we have designed intramolecularly stabilized silylium ions whose electron deficiency is attenuated by an adjacent, electron-rich ferrocenyl fragment. Here we wish to present the synthesis and structural characterization of these unique transition metal-stabilized silicon cations which reveal an unprecedented bonding situation different from its isoelectronic analogues. The potential of this motif is further highlighted in challenging Diels–Alder reactions, which are catalyzed at low temperatures with exceptional reaction rates and selectivities.
Dithiol Proteins as Guardians of the Intracellular Redox Milieu in Parasites: Old and New Drug Targets in Trypanosomes and Malaria‐Causing Plasmodia (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Synthesis of Copper Sulfide Nanorod Arrays on Molecular Templates (2004)

We investigate the making of semiconductor nanorods using well-defined molecular templates. The films are characterized by AFM and XPS. The spin-coated monolayer of arachidic acid assembles on graphite as 1D nanostripes with bilayer periodicity. The copper arachidate film shows curved stripes, which become straight after reacting with hydrogen sulfide. The new template scheme may facilitate the fabrication of nanorod arrays of a variety of inorganic and semiconducting materials.
Effect of ozone treatment on reactive oxygen species and adenosine production during hepatic ischemia-reperfusion (2000)

This study investigates whether ozone could confer protection from hepatic ischemia reperfusion by modifying the accumulation of adenosine and xanthine during ischemia. A significant increase in both adenosine and xanthine accumulation was observed as a consequence of ATP degradation during hepatic ischemia. Adenosine exerts a protective effect on hepatic ischemia reperfusion injury since the elimination of endogenous adenosine accumulation with adenosine deaminase increased the hepatic injury associated with this process. On the other hand, the high xanthine levels observed after ischemia could exert deleterious effects during reperfusion due to reactive oxygen species generation from xanthine oxidase. The administration of allopurinol, an inhibitor of xanthine oxidase, attenuated the increase in reactive oxygen species and transaminase levels observed after hepatic reperfusion. Ozone treatment in liver maintained adenosine levels similar to those found after ischemia but led to a marked reduction in xanthine accumulation. In order to evaluate the role of both adenosine and xanthine, we tried to modify the protection confered by ozone, by modifying the concentrations of adenosine and xanthine. The metabolization of endogenous adenosine after ischemia abolished the protective effect conferred by ozone. When xanthine was administered previous to ozone treatment, the protection conferred by adenosine disappeared, showing both postischemic reactive oxygen species and transaminase levels similar to those found after hepatic ischemia reperfusion. Ozone would confer protection against the hepatic ischemia reperfusion injury by the accumulation of adenosine that in turns benefits the liver and by blocking the xanthine/xanthine oxidase pathway for reactive oxygen species generation.
Submicrometer Chemical Patterning with High Throughput Using Magnetolithography (2009)

This letter demonstrates the ability to pattern surfaces chemically with submicrometer resolution by applying the simple and inexpensive magnetolithography (ML) method. This method allows fast patterning of large surfaces without having to face contamination problems or the need to remove the substrate from the solution. With ML it is possible to obtain pattern whose width is narrower than the width of the lines in the mask. By applying the green fluorescent protein (GFP), we were able to probe a 30 nm line of hydrophobic molecules patterned on a substrate coated with a hydrophilic monolayer.
Low plasma concentrations of VIP and elevated levels of other neuropeptides during exacerbations of asthma (1994)

Neuropeptides in the lung occur in neurons, neuroendocrine and inflammatory cells. Their widespread distribution and physiological effects suggest that they may play important roles in asthma. We investigated whether, during an exacerbation of asthma, patients displayed changes in plasma levels of the neuropeptides vasoactive intestinal peptide (VIP), calcitonin gene-related peptide (CGRP), substance P (SP), and neuropeptide Y (NPY). Venous blood from 25 adult patients attending the emergency ward with an exacerbation of asthma was sampled before and after treatment. Plasma levels of VIP-, SP-, CGRP- and NPY-like immunoreactivity (-LI) were determined by immunoassay, and the results obtained were compared with findings in 21 healthy controls. The mean plasma levels of VIP-LI were lower in patients (3.4 +/- 0.4 pmol.l-1) than in controls (10.4 +/- 0.7 pmol.l-1), whereas the levels of CGRP-LI (43.7 +/- 3.4 pmol.l-1), SP-LI (4.6 +/- 0.4 pmol.l-1) and NPY-LI levels (159 +/- 6 pmol.l-1) were higher in patients than in controls (21.1 +/- 3.4; 2.2 +/- 0.2 and 105 +/- 8 pmol.l-1, respectively). A relationship was seen between the reversibility of obstruction, expressed as improvement of peak expiratory flow upon treatment, and the neuropeptide levels, such that lower VIP-LI levels and higher CGRP-LI levels correlated with less reversibility. Plasma levels of neuropeptides, VIP-LI and CGRP-LI in particular, may therefore be employed as predictors of responsiveness to bronchodilatory therapy.