gebhart/patrepeval huggingface dataset:
Fucoidan Is the Active Component of Fucus vesiculosus that Promotes Contraction of Fibroblast-Populated Collagen Gels. (2000)

The fibroblast-populated collagen gel culture method has been evaluated as a dermal model of wound contraction and granulation in tissues during the wound healing process and as an in vitro model of dermal tissue. We previously reported that an extract of Fucus vesiculosus promoted fibroblast-populated collagen gel contraction and that the promotion of the gel contraction was due to the increased expression of integrin alpha2beta1 on the surface of the fibroblasts. In this study, we investigated the active component of the extract of this alga using extraction and fractionation techniques. Water extraction of the alga was followed by precipitation with excess ethanol and then gel filtration with the boundary molecular weight of 30,000. The high molecular weight fraction obtained from gel filtration was fractionated by ion exchange chromatography on diethylaminoethyl cellulose column to give active fractions that have more polar properties. These polar, high molecular weight fractions which contained molecules with fucose and sulfate groups showed significant gel contraction-promoting activity and integrin expression-enhancing activity, and were estimated to be the sulfated-polysaccharide fucoidan. Commercially available fucoidan showed similar activities to the above-described fraction of this alga. Although it remains necessary to precisely identify the specific active component, the above results indicate that fucoidan is the active component which promotes collagen gel contraction, and also indicate the possibility that it dose so by enhancing the integrin alpha2beta1 expression.
Single Parameter Model for Cosmic Scale Photon Redshift in a Closed Universe (2021)

A successful single parameter model has been formulated to match the observations of photons from type 1a supernovae which were previously used to corroborate the standard &#120556 cold dark matter model. The new single parameter model extrapolates all the way back to the cosmic background radiation (CMB) without requiring a separate model to describe inflation of the space dimensions after the Big Bang. This single parameter model assumes that spacetime forms a finite symmetrical manifold with positive curvature. For the spacetime manifold to be finite, the time dimension must also have positive curvature. This model was formulated to consider whether the curvature of the time dimension may be related to the curvature of the space dimensions. This possibility is not considered in the more complex models previously used to fit the available redshift data. The geometry for the finite spacetime manifold was selected to be compatible with the Friedmann equation with positive curvature. The manifold shape was motivated by an assumption that there exists a matter hemisphere (when considering time together with a single space dimension) and an antimatter hemisphere to give a symmetrical and spherical overall spacetime manifold. Hence, the space dimension expands from a pole to the equator, at a maximum value for the time dimension. This is analogous to the expansion of a circle of latitude on a globe from a pole to the equator. The three space dimensions are identical so that any arbitrary single space direction may be selected. The initial intention was to modify the assumed geometry for the spacetime manifold to account for the presence of matter. It was surprisingly found that, within the error of the reported measurements, no further modification was necessary to fit the data. The Friedmann equation reduces to the Schwarzschild equation at the equator so this can be used to predict the total amount of mass in the Universe. The resulting prediction is of the order of 1051 kg. The corresponding density of matter at the current time is approximately 1.6 × 10-28 kg·m-3.
Chemical Synthesis of Intentionally Misfolded Homogeneous Glycoprotein: A Unique Approach for the Study of Glycoprotein Quality Control (2012)

Biosynthesis of glycoproteins in the endoplasmic reticulum employs a quality control system, which discriminates and excludes misfolded malfunctional glycoproteins from a correctly folded one. As chemical tools to study the glycoprotein quality control system, we systematically synthesized misfolded homogeneous glycoproteins bearing a high-mannose type oligosaccharide via oxidative misfolding of a chemically synthesized homogeneous glycopeptide. The endoplasmic reticulum folding sensor enzyme, UDP-glucose:glycoprotein glucosyltransferase (UGGT), recognizes a specific folding intermediate, which exhibits a molten globule-like hydrophobic nature.
Abstract 19302: Surgical Approach to Continuous Flow Left Ventricular Assist Device Explantation: a Comparison of Outcomes (2014)

Objective: Weaning and explanation of selected patients with continuous flow left ventricular assist devices (CF LVADs) has been shown to be feasible. Clinical outcomes are poorly described regarding the various operative approaches employed, which differ primarily in the degree of retained pump material. We evaluate the impact of CF LVAD explant surgical approach on early and late clinical events. Methods: A single-center, retrospective review was performed, evaluating all patients who underwent explanation of a CF LVAD (2006-2014). Descriptive univariate statistics, multivariate regression and survival analysis were performed. Patients were stratified by surgical approach, and censored by transplant, device re-implantation or death. Results: A total of 27 patients were identified (25 HeartMateII, 2 HeartWare); characteristics and outcomes are listed in Figure 1a. Four approaches were used: complete pump and outflow excision with ventriculotomy closure (n=13 ; 48%), pump excision and ligation of inflow and outflow grafts (n=7 ; 26%), ligation of outflow graft and driveline transection (n=5 ; 19%), or driveline transection alone (n=2 ; 7%). Primary incisions were subcostal (n=19, 70%) or subxiphoid (n=5, 19%), with 1 conversion to sternotomy (n=1, 7%). Mean duration of CF support prior to explant was 532±424 days (range 42-1937 days), while post-explant survival (defined as time preceding transplant, device re-implantation, or death) was 1116±927 days (range 127-2877 days). Survival stratified by surgical approach is shown in Figure 1b. Overall time-to-event and survival analyses showed no significant difference in postoperative length of stay (p=0.7), stroke (p=0.12), reoperation (p=0.4), or total survival (p=0.12) between surgical approaches. Conclusions: This is the largest description of CF LVAD explantation by surgical approach. While technical difficulty varies, all are feasible with similar early and late survival and clinical outcomes.
DNA Shape Dominates Sequence Affinity in Nucleosome Formation (2014)

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.
Fabrication and analysis of vertical p-type InAs-Si nanowire Tunnel FETs (2015)

We report InAs-Si nanowire (NW) Tunnel FETs fabricated inside nanotube templates. High device yield and performances are obtained by optimizing the growth conditions and the fabrication flow using inorganic material as dielectric spacer, atomic-layer-deposition for the metal gate and by scaling the equivalent oxide thickness (EOT). We extract the exponential parameter B of Kane's tunneling model for direct bandgap (E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> ) materials and compare it with experimental results. Moreover, studying the activation energy (E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A</sub> ) for TFETs with different EOTs allows us to distinguish the different conduction mechanisms.
Remote Control of Multimodal Nanoscale Ligand Oscillations Regulates Stem Cell Adhesion and Differentiation (2017)

Cellular adhesion is regulated by the dynamic ligation process of surface receptors, such as integrin, to adhesive motifs, such as Arg-Gly-Asp (RGD). Remote control of adhesive ligand presentation using external stimuli is an appealing strategy for the temporal regulation of cell-implant interactions in vivo and was recently demonstrated using photochemical reaction. However, the limited tissue penetration of light potentially hampers the widespread applications of this method in vivo. Here, we present a strategy for modulating the nanoscale oscillations of an integrin ligand simply and solely by adjusting the frequency of an oscillating magnetic field to regulate the adhesion and differentiation of stem cells. A superparamagnetic iron oxide nanoparticle (SPION) was conjugated with the RGD ligand and anchored to a glass substrate by a long flexible poly(ethylene glycol) linker to allow the oscillatory motion of the ligand to be magnetically tuned. In situ magnetic scanning transmission electron microscopy and atomic force microscopy imaging confirmed the nanoscale motion of the substrate-tethered RGD-grafted SPION. Our findings show that ligand oscillations under a low oscillation frequency (0.1 Hz) of the magnetic field promoted integrin-ligand binding and the formation and maturation of focal adhesions and therefore the substrate adhesion of stem cells, while ligands oscillating under high frequency (2 Hz) inhibited integrin ligation and stem cell adhesion, both in vitro and in vivo. Temporal switching of the multimodal ligand oscillations between low- and high-frequency modes reversibly regulated stem cell adhesion. The ligand oscillations further induced the stem cell differentiation and mechanosensing in the same frequency-dependent manner. Our study demonstrates a noninvasive, penetrative, and tunable approach to regulate cellular responses to biomaterials in vivo. Our work not only provides additional insight into the design considerations of biomaterials to control cellular adhesion in vivo but also offers a platform to elucidate the fundamental understanding of the dynamic integrin-ligand binding that regulates the adhesion, differentiation, and mechanotransduction of stem cells.
MO890: Modifiable and Non-Modifiable Factors Associated With Increased COVID-19 Related Mortality Among Dialysis Patients (2022)

Abstract BACKGROUND AND AIMS Patients with end-stage kidney disease (ESKD) face higher risk for severe outcomes from COVID-19 infection. Moreover, it is not well known to which extent potentially modifiable risk factors contribute to mortality risk. In this study, we investigated the incidence and risk factors for 30-day case-fatality of COVID-19 in haemodialysis patients treated in the European Fresenius Medical Care (FMC) Nephrocare network. METHOD In this historical cohort study, we included unvaccinated adult dialysis patients with a first documented SARS-CoV-2 infection between 1 February 2020 and 31 March 2021 (study period) registered in the European Clinical Database (EuCliD®). The first SARS-CoV-2 suspicion date for all documented infections was considered the index date for the analysis. Patients were followed for up to 30 days. Follow-up time was defined from the index date until the date of death, end of follow-up period or lost to follow-up, whichever occurred first. We ascertained patients’ characteristics in the 6-month period prior to index date. We used logistic regression and XGBoost to assess risk factors for 30-day mortality. RESULTS We included 9211 patients meeting the inclusion criteria for the study (Table 1). Age was 65.4 ± 13.7 years, dialysis vintage was 4.2 ± 3.7 years. In the follow up period, 1912 patients died within 30 days (20.8%, 95% confidence interval: 19.9%–21.6%). Correlates of COVID-19 related mortality are summarized in Table 2. Several potentially modifiable factors were associated with increased risk of death: patients on HD compared with online haemodiafiltration had shorter survival after presentation with COVID-19 as well as those who did not achieve the therapeutic targets for serum albumin, erythropoietin resistance index, protein catabolic rate, haemodynamic status, C-reactive protein, single-pool Kt/V, hydration status and serum sodium in the months before infection. The discrimination accuracy of prediction models developed with XGBoost was similar to that observed for main-effect logistic regression (AUC 0.69 and 0.71, respectively) suggesting that no major cross-interaction and non-linear effect could improve prediction accuracy. CONCLUSION We observed high 30-day COVID-19 related mortality among unvaccinated dialysis patients. Older patients, men and those with greater comorbidities had higher risk of death after COVID-19 infection. Derangement in potentially modifiable factors in the 6 months prior to COVID-19 infection was independently associated with increased mortality. Whether achievement of clinical therapeutic targets is associated with improved survival after COVID-19 infection is a matter of further research.
Mesoporous Magnetic Cysteine Functionalized Chitosan Nanocomposite for Selective Uranyl Ions Sorption: Experimental, Structural Characterization, and Mechanistic Studies (2022)

Nuclear power facilities are being expanded to satisfy expanding worldwide energy demand. Thus, uranium recovery from secondary resources has become a hot topic in terms of environmental protection and nuclear fuel conservation. Herein, a mesoporous biosorbent of a hybrid magnetic-chitosan nanocomposite functionalized with cysteine (Cys) was synthesized via subsequent heterogeneous nucleation for selectively enhanced uranyl ion (UO<sub>2</sub><sup>2+</sup>) sorption. Various analytical tools were used to confirm the mesoporous nanocomposite structural characteristics and confirm the synthetic route. The characteristics of the synthesized nanocomposite were as follows: superparamagnetic with saturation magnetization (<i>M</i><sub>S</sub>: 25.81 emu/g), a specific surface area (S<sub>BET</sub>: 42.56 m<sup>2</sup>/g) with a unipore mesoporous structure, an amine content of ~2.43 mmol N/g, and a density of ~17.19/nm<sup>2</sup>. The experimental results showed that the sorption was highly efficient: for the isotherm fitted by the Langmuir equation, the maximum capacity was about 0.575 mmol U/g at pH range 3.5-5.0, and Temperature (25 ± 1 °C); further, there was excellent selectivity for UO<sub>2</sub><sup>2+</sup>, likely due to the chemical valent difference. The sorption process was fast (~50 min), simulated with the pseudo-second-order equation, and the sorption half-time (t<sub>1/2</sub>) was 3.86 min. The sophisticated spectroscopic studies (FTIR and XPS) revealed that the sorption mechanism was linked to complexation and ion exchange by interaction with S/N/O multiple functional groups. The sorption was exothermic, spontaneous, and governed by entropy change. Desorption and regeneration were carried out using an acidified urea solution (0.25 M) that was recycled for a minimum of six cycles, resulting in a sorption and desorption efficiency of over 91%. The as-synthesized nanocomposite's high stability, durability, and chemical resistivity were confirmed over multiple cycles using FTIR and leachability. Finally, the sorbent was efficiently tested for selective uranium sorption from multicomponent acidic simulated nuclear solution. Owing to such excellent performance, the Cys nanocomposite is greatly promising in the uranium recovery field.
The CAM Model for CIC-DUX4 Sarcoma and Its Potential Use for Precision Medicine (2021)

(1) Background: <i>CIC-DUX4</i> sarcoma is a rare mesenchymal small round cell tumor which belongs to rare cancers that occupy a significant percentage of cancer cases as a whole, despite each being rare. Importantly, each rare cancer type has different features, and thus there is a need to develop a model that mimics the features of each of these cancers. We evaluated the idea that the chicken chorioallantoic membrane assay (CAM), a convenient and versatile animal model, can be established for the <i>CIC-DUX4</i> sarcoma. (2) Methods: Patient-derived cell lines of <i>CIC-DUX4</i> were applied. These cells were transplanted onto the CAM membrane and tumor formation was examined by H&E staining, immunohistochemistry and Western blotting. The CAM tumor was transferred onto a fresh CAM and was also used to form organoids. Retention of the fusion gene was examined. (3) Results: H&E staining as well as molecular characterization demonstrated the formation of the <i>CIC-DUX4</i> tumor on the CAM membrane. Expression of cyclin D2 and ETV4 was identified. The CAM tumor was transferred to a fresh CAM to form the second-generation CAM tumor. In addition, we were successful in forming tumor organoids using the CAM tumor. Retention of the fusion gene <i>CIC-DUX4</i> in the CAM, second-generation CAM, and in the CAM-derived organoids was confirmed by RT-PCR. (4) Conclusions: The CAM assay provides a promising model for <i>CIC-DUX4</i> sarcoma.
Randomness Complexity of Private Circuits for Multiplication. (2016)

Many cryptographic algorithms are vulnerable to side channel analysis and several leakage models have been introduced to better understand these flaws. In 2003, Ishai, Sahai and Wagner introduced the d-probing security model, in which an attacker can observe at most d intermediate values during a processing. They also proposed an algorithm that securely performs the multiplication of 2 bits in this model, using only $$dd+1/2$$dd+1/2 random bits to protect the computation. We study the randomness complexity of multiplication algorithms secure in the d-probing model. We propose several contributions: we provide new theoretical characterizations and constructions, new practical constructions and a new efficient algorithmic tool to analyze the security of such schemes.

We start with a theoretical treatment of the subject: we propose an algebraic model for multiplication algorithms and exhibit an algebraic characterization of the security in the d-probing model. Using this characterization, we prove a linear in d lower bound and a quasi-linear non-constructive upper bound for this randomness cost. Then, we construct a new generic algorithm to perform secure multiplication in the d-probing model that only uses $$d + d^2/4$$d+d2/4 random bits.

From a practical point of view, we consider the important cases $$d \le 4$$d≤4 that are actually used in current real-life implementations and we build algorithms with a randomness complexity matching our theoretical lower bound for these small-order cases. Finally, still using our algebraic characterization, we provide a new dedicated verification tool, based on information set decoding, which aims at finding attacks on algorithms for fixed order d at a very low computational cost.
Transitions Between Circulatory States After Out-of-Hospital Cardiac Arrest: Protocol for an Observational, Prospective Cohort Study (Preprint) (2017)

<sec> <title>BACKGROUND</title> The post cardiac arrest syndrome (PCAS) is responsible for the majority of in-hospital deaths following cardiac arrest (CA). The major elements of PCAS are anoxic brain injury and circulatory failure. </sec> <sec> <title>OBJECTIVE</title> This study aimed to investigate the clinical characteristics of circulatory failure and inflammatory responses after out-of-hospital cardiac arrest (OHCA) and to identify patterns of circulatory and inflammatory responses, which may predict circulatory deterioration in PCAS. </sec> <sec> <title>METHODS</title> This study is a single-center cohort study of 50 patients who receive intensive care after OHCA. The patients are followed for 5 days where detailed information from circulatory variables, including measurements by pulmonary artery catheters (PACs), is obtained in high resolution. Blood samples for inflammatory and endothelial biomarkers are taken at inclusion and thereafter daily. Every 10 min, the patients will be assessed and categorized in one of three circulatory categories. These categories are based on mean arterial pressure; heart rate; serum lactate concentrations; superior vena cava oxygen saturation; and need for fluid, vasoactive medications, and other interventions. We will analyze predictors of circulatory failure and their relation to inflammatory biomarkers. </sec> <sec> <title>RESULTS</title> Patient inclusion started in January 2016. </sec> <sec> <title>CONCLUSIONS</title> This study will obtain advanced hemodynamic data with high resolution during the acute phase of PCAS and will analyze the details in circulatory state transitions related to circulatory failure. We aim to identify early predictors of circulatory deterioration and favorable outcome after CA. </sec> <sec> <title>CLINICALTRIAL</title> ClinicalTrials.gov: NCT02648061; https://clinicaltrials.gov/ct2/show/NCT02648061 (Archived by WebCite at http://www.webcitation.org/6wVASuOla) </sec>
Cloud Reference Framework (2015)

This document presents a cloud reference framework that intends to
provide a basis for designing interoperable cloud services and their
integration into existing open Internet and enterprise IT
infrastructures. In general, a cloud-based system utilizes
virtualized computing / communications / storage resources and
applications, and allows their combined provisioning as complex
infrastructure services. In the emerging cloud-based virtualized
infrastructures and services are provisioned on on-demand basis, and
configured for specific customer needs or tasks. The reference
framework is based on the survey of the SDOs and WGs that are focusing
on cloud-based systems and services (Cloud SDO, I-D.Khasnabish-cloud-
sdo-survey), on-going standardisation activities and other research
and developments in the cloud computing technology area. Both intra-
cloud and inter-cloud reference frameworks are presented and the
requirements to the general functional layers and components are
discussed.