gebhart/patrepeval huggingface dataset:
The intragenus and interspecies quorum-sensing autoinducers exert distinct control over Vibrio cholerae biofilm formation and dispersal (2019)

Vibrio cholerae possesses multiple quorum-sensing (QS) systems that control virulence and biofilm formation among other traits. At low cell densities, when QS autoinducers are absent, V. cholerae forms biofilms. At high cell densities, when autoinducers have accumulated, biofilm formation is repressed, and dispersal occurs. Here, we focus on the roles of two well-characterized QS autoinducers that function in parallel. One autoinducer, called cholerae autoinducer-1 (CAI-1), is used to measure Vibrio abundance, and the other autoinducer, called autoinducer-2 (AI-2), is widely produced by different bacterial species and presumed to enable V. cholerae to assess the total bacterial cell density of the vicinal community. The two V. cholerae autoinducers funnel information into a shared signal relay pathway. This feature of the QS system architecture has made it difficult to understand how specific information can be extracted from each autoinducer, how the autoinducers might drive distinct output behaviors, and, in turn, how the bacteria use QS to distinguish kin from nonkin in bacterial communities. We develop a live-cell biofilm formation and dispersal assay that allows examination of the individual and combined roles of the two autoinducers in controlling V. cholerae behavior. We show that the QS system works as a coincidence detector in which both autoinducers must be present simultaneously for repression of biofilm formation to occur. Within that context, the CAI-1 QS pathway is activated when only a few V. cholerae cells are present, whereas the AI-2 pathway is activated only at much higher cell density. The consequence of this asymmetry is that exogenous sources of AI-2, but not CAI-1, contribute to satisfying the coincidence detector to repress biofilm formation and promote dispersal. We propose that V. cholerae uses CAI-1 to verify that some of its kin are present before committing to the high-cell-density QS mode, but it is, in fact, the broadly made autoinducer AI-2 that sets the pace of the V. cholerae QS program. This first report of unique roles for the different V. cholerae autoinducers suggests that detection of kin fosters a distinct outcome from detection of nonkin.
ChemInform Abstract: Enzymatic Resolution of 1,2‐Diols: Comparison Between Hydrolysis and Transesterification Reactions. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
SkiVis: Visual Exploration and Route Planning in Ski Resorts (2023)

Optimal ski route selection is a challenge based on a multitude of factors, such as the steepness, compass direction, or crowdedness. The personal preferences of every skier towards these factors require individual adaptations, which aggravate this task. Current approaches within this domain do not combine automated routing capabilities with user preferences, missing out on the possibility of integrating domain knowledge in the analysis process. We introduce SkiVis, a visual analytics application to interactively explore ski slopes and provide routing recommendations based on user preferences. In collaboration with ski guides and enthusiasts, we elicited requirements and guidelines for such an application and propose different workflows depending on the skiers' familiarity with the resort. In a case study on the resort of Ski Arlberg, we illustrate how to leverage volunteered geographic information to enable a numerical comparison between slopes. We evaluated our approach through a pair-analytics study and demonstrate how it supports skiers in discovering relevant and preference-based ski routes. Besides the tasks investigated in the study, we derive additional use cases from the interviews that showcase the further potential of SkiVis, and contribute directions for further research opportunities.
Notice of Removal: High-resolution vector Doppler for cerebral blood flow estimation (2017)

Removed.
The effect of cross-links on the conformational dynamics of duplex DNA (1997)

The base pair lifetimes and apparent dissociation constants of a 21 base DNA hairpin and an analog possessing a disulfide cross-link bridging the 3'- and 5'-terminal bases were determined by measuring imino proton exchange rates as a function of exchange catalyst concentration and temperature. A comparison of the lifetimes and apparent dissociation constants for corresponding base pairs of the two hairpins indicates that the cross-link neither increases the number of base pairs involved in fraying nor alters the lifetime, dissociation constant, or the opened structure from which exchange occurs for the base pairs that are not frayed. The cross-link does, however, stabilize the frayed penultimate base pair of the stem duplex. Significantly, it appears that the disulfide cross-link is more effective at preventing fraying of the penultimate base pair than is the 5 base hairpin loop. Because this disulfide cross-link can be incorporated site specifically, and does not adversely affect static or dynamic properties of DNA, it should prove very useful in studies of nucleic acid structure and function.
Nylon Foil (Supramid) Orbital Implants in Pediatric Orbital Fracture Repair (2014)

The nylon foil implant is a safe and effective method to repair pediatric orbital wall fractures given the low complication rate.
C9orf72 poly(GR) aggregation induces TDP-43 proteinopathy (2020)

TAR DNA-binding protein 43 (TDP-43) inclusions are a pathological hallmark of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), including cases caused by G<sub>4</sub>C<sub>2</sub> repeat expansions in the <i>C9orf72</i> gene (c9FTD/ALS). Providing mechanistic insight into the link between <i>C9orf72</i> mutations and TDP-43 pathology, we demonstrated that a glycine-arginine repeat protein [poly(GR)] translated from expanded G<sub>4</sub>C<sub>2</sub> repeats was sufficient to promote aggregation of endogenous TDP-43. In particular, toxic poly(GR) proteins mediated sequestration of full-length TDP-43 in an RNA-independent manner to induce cytoplasmic TDP-43 inclusion formation. Moreover, in GFP-(GR)<sub>200</sub> mice, poly(GR) caused the mislocalization of nucleocytoplasmic transport factors and nuclear pore complex proteins. These mislocalization events resulted in the aberrant accumulation of endogenous TDP-43 in the cytoplasm where it co-aggregated with poly(GR). Last, we demonstrated that treating G<sub>4</sub>C<sub>2</sub> repeat-expressing mice with repeat-targeting antisense oligonucleotides lowered poly(GR) burden, which was accompanied by reduced TDP-43 pathology and neurodegeneration, including lowering of plasma neurofilament light (NFL) concentration. These results contribute to clarification of the mechanism by which poly(GR) drives TDP-43 proteinopathy, confirm that G<sub>4</sub>C<sub>2</sub>-targeted therapeutics reduce TDP-43 pathology in vivo, and demonstrate that alterations in plasma NFL provide insight into the therapeutic efficacy of disease-modifying treatments.
Investigation of hemodynamics during cardiopulmonary bypass: A multiscale multiphysics fluid–structure-interaction study (2016)

Neurological complications often occur during cardiopulmonary bypass (CPB). Hypoperfusion of brain tissue due to diminished cerebral autoregulation (CA) and thromboembolism from atherosclerotic plaque reduce the cerebral oxygen supply and increase the risk of perioperative stroke. To improve the outcome of cardiac surgeries, patient-specific computational fluid dynamic (CFD) models can be used to investigate the blood flow during CPB. In this study, we establish a computational model of CPB which includes cerebral autoregulation and movement of aortic walls on the basis of in vivo measurements. First, the Baroreflex mechanism, which plays a leading role in CA, is represented with a 0-D control circuit and coupled to the 3-D domain with differential equations as boundary conditions. Additionally a two-way coupled fluid-structure interaction (FSI) model with CA is set up. The wall shear stress (WSS) distribution is computed for the whole FSI domain and a comparison to rigid wall CFD is made. Constant flow and pulsatile flow CPB is considered. Rigid wall CFD delivers higher wall shear stress values than FSI simulations, especially during pulsatile perfusion. The flow rates through the supraaortic vessels are almost not affected, if considered as percentages of total cannula output. The developed multiphysic multiscale framework allows deeper insights into the underlying mechanisms during CPB on a patient-specific basis.
A Critique of the Intraoperative Use of Jugular Venous Bulb Catheters During Neurosurgical Procedures (1994)

We examined the intraoperative use of jugular venous bulb catheters in 100 consecutive patients undergoing neurosurgical procedures. The catheters were successfully placed after induction of anesthesia in 99 patients using an aseptic technique. The efforts were abandoned after four attempts in the remaining patient. The mean time of insertion was 94 s (SD 108, range 15-420). Carotid artery puncture on two occasions controlled by firm pressure was the only complication. Arterial blood pressure, PaCO2, PaO2, and jugular venous bulb oxygen saturations (SjVO2) were intermittently measured at set intervals throughout the operation. We defined cerebral venous desaturation as 1) none (SjVO2 > 50%), 2) mild (45% < SjVO2 < 50%), and 3) severe (SjVO2 < 45%). We graded the usefulness of the catheter as 1) not useful (NU), SjVO2 > 50% and PaCO2 > 25 mm Hg; 2) useful (U1), SjVO2 > 50% and PaCO2 < 25 mm Hg; intervention, no increase in PaCO2; 3) useful (U2), SjVO2 < 50% and PaCO2 < 25 mm Hg; intervention, increase PaCO2 to improve SjVO2; 4) useful (U3), SjVO2 < 50% and PaCO2 > 25 mm Hg; intervention, nonventilatory action to increase SjVO2 (e.g., infusion of mannitol). Mild desaturation was detected in 24 patients and severe desaturation was present in 17 patients. We found SjVO2 monitoring to be useful in 60 of 99 patients studied. It was useful for detecting and treating cerebral venous desaturation in 13 of 18 patients with intracranial hematomas (subdural, epidural, and intracerebral hematomas), 9 of 18 patients with intracerebral tumors, 27 of 45 patients with cerebral aneurysms, and 6 of 8 patients with other intracranial pathology.(ABSTRACT TRUNCATED AT 250 WORDS)
Four-color multiparameter DNA flow cytometric method to study phenotypic intratumor heterogeneity in cervical cancer (2000)

PI is a superior DNA stain to TP3 when using intact normal PBL and human cancer cells. Four-color high-resolution multiparameter DNA flow cytometry allows the identification of intratumor subpopulations using PI as DNA stain and FITC, RPE, and APC as reporter molecules. The FACSCalibur bench-top flow cytometer can be used for this purpose, allowing the application of this technique in clinical laboratories.
Toward Separating Integer Factoring from Discrete Logarithm mod p (2007)

This paper studies the reduction among cyptographic functions. Our main result is that the prime factoring function IF does not reduce to the certified discrete logarithm function modulo a prime nor its variant with respect to some special reducibility, i.e. the range injection reducibility, under the assumption that the Heath-Brown conjecture is true and IF â PF. Since there is no known direct relationship between these functions, this is the first result that could separate these functions. Our approach is based on the notion of the preimage functions.
Demonstration of Standard IPTV Content Delivery Network Architecture Interfaces: Prototype of Standardized IPTV Unicast Content Delivery Server Selection Mechanisms (2009)

In this document we suggest a demonstration of standard SIP/RTSP based content delivery networks (CDN). The intended use of SIP based CDNs is in the scope of IMS based IPTV architectures that are being standardized in the open IPTV forum [1], ESTI-TISPAN and the ITU-T. The system includes a central server (content delivery network controller) analyzing all received content delivery requests. The content delivery network controller chooses the cluster of servers a request should be redirected to. The choice is made depending on client location, content availability, location and servers' global load. Each cluster is controlled by a cluster controller that would make the choice of the final VoD server to deliver the content, based on a fine grained analysis of the load of the VoD servers it manages. The system proves the feasibility of the standards and highlights the flexibility of SIP [1] interfaces when coupled with RTSP [2] to organize redirections within a CDN.
P‐12: Enhanced Pentacene OTFTs with Suspended Source/Drain Electrode (2007)

Abstract We have proposed and fabricated a new triisopropylsilyl (TIPS) pentacene organic thin‐film transistor (OTFT) by employing suspended source/drain (SSD) electrode which successfully improves the electrical properties such as field‐effect mobility, on/off ratio, threshold voltage (V TH ) and subthreshold slope compared to conventional bottom‐contact OTFTs. The SSD electrode was fabricated by using Cr/Au double layer where the Cr was used as a sacrificial layer. By completely etching the Cr layer in the active area, a suspended Au source/drain structure is constructed forming a top‐contact‐like geometry. The field‐effect mobility of ink‐jet printed TIPS pentacene OTFT increased from 0.007 cm 2 /Vs to 0.066 cm 2 /Vs, on/off ratio increased from 10 4 to 10 6 , V TH decreased from +9 V to −3 V and subthreshold slope decreased from 4.5 V/decade to 0.9 V/decade.
Modeling and measurement of the vibrational response of the ovine head as it relates to intracranial pressure (1996)

A combined experimental and analytical approach was taken to understand the vibrational characteristics of the ovine head, as a framework to use vibrational measurements to monitor changes in intracranial pressure. Modal analysis was performed on excised ovine heads to establish the spatial and spectral behavior of the head as a function of the presence of the soft extracranial and intracranial tissues and boundary conditions. Measurements of ovine cranial bone thickness, density, moisture content, and modulus of elasticity provided material property values for incorporation into analytical models of the ovine skull. Simplified spherical models were used in a parametric analysis to determine the sensitivity of the skull to changes in material properties and geometry. A detailed finite element model of the ovine skull was obtained by digitizing the cranial cavity of an ovine skull in 3D. Isotropic, homogeneous material properties which were measured for ovine cranial bone were incorporated into the detailed geometric model. The calculated modal shapes from the finite element model were validated by high correlations to experimental modal shapes as calculated by the Modal Assurance Criterion. While the finite element model described the vibrational behavior of the head adequately, it was relatively insensitive to increases in internal pressure of 50 cm H2O.
A Novel Family of Biodegradable Poly(ester amide) Elastomers (2011)

Biodegradable elastomeric materials have particular utility in tissue engineering applications because their compliance under force closely resembles the elastic nature of many human tissues. A family of biodegradable poly(ester amide) elastomers were developed, with excellent elasticity under hydrated conditions, good in vivo biocompatibility and a slow degradation rate. This study sheds light on the structure-property relationship behind designing biodegradable elastomeric materials.
Versatile Selective α-CarboxylicAcid Esterification of N-Protected Amino Acids and Peptides by Alcalase (2009)

Under continuous removal of water, the industrial protease Alcalase allows selective synthesis of α-carboxylic acid methyl, ethyl, benzyl, allyl, 2-(trimethylsilyl)ethyl, and tert-butyl esters of amino acids and peptides under mild conditions in very high yields. The purified yields range from 72% to 92%.
Numerical Research and Open Sea Tests of a 100 kW Modified Edinburgh Duck Wave Energy Convertor (2019)

This paper presents a modified wave energy device. The wave energy device retains the primitive capture shape of the famous Edinburgh Duck, but uses a new underwater stabilized substrate. The hydrodynamic calculation with frequency-domain models was performed to find out the optimum wave period for the wave energy converter. The results in this paper were obtained by using the Boundary Element Method (BEM). The characteristic function expands of velocity potential in the cylindrical coordinate system was applied to limit computational domain and improve computational speed. The hydrodynamic performance of the device was assessed. The influence of hydraulic damping coefficient was evaluated. Focus was given to the capture width ratio, motion of the device and optimal hydraulic damping coefficient. After 2 years of construction in the shipyard, the device was constructed and an open sea test had been finished near WanShan Island, South China Sea. During the test, the daily power generation and power curve of the device were measured.
The dream of synthetic life generates recombinant organisms endowed with unpredictable risks ("El sueño de la razón produce monstruos") (2011)

This text answer the question, posted by the editor, on the philosophical, scientific and social problems followed from the synthetic ensemble of the modified genome of the bacteria M. Mycoides, announced in May 2010 by the J. Craig Venter Institute.
Comparison of Children Hospitalized With Seasonal Versus Pandemic Influenza A, 2004–2009 (2012)

pH1N1 in children differed from seasonal influenza A in risk factors, clinical presentation, and length of hospital stay, but not ICU admission or mortality.
Elastohydrodynamics of Roll-to-Roll UV-Cure Imprint Lithography (2019)

Inextensible cylindrical shell theory and lubrication theory combine into a model for the elastohydrodynamics of a rolling-imprint modality of nanoimprint lithography (NIL). Foil-bearing theory describes the formation of the lubrication gap due to relative motion between a tensioned substrate and a rigid, cylindrical surface. Reproduction of the results of foil-bearing theory for both stiff and perfectly-flexible substrates validates this coupled model and reveals a highly predictable region of uniformity that provides low shear stress conditions ideal for UV-cure. Here, these results show theoretical limitations that are used to construct an operating window for predicting rolling-mode NIL process feasibility.
DNA methylation status is inversely correlated with green tea intake and physical activity in gastric cancer patients (2008)

Epigenetic silencing of genes by aberrant DNA methylation is recognized as a crucial component of the mechanism underlying tumorigenesis. However, the relationship between DNA methylation and the past lifestyle in cancer patients remains largely unknown. We examined the methylation statuses of 6 tumor-related genes, CDX2 (homeobox transcription factor), BMP-2 (bone morphogenetic protein 2), p16 (INK4A), CACNA2D3 (calcium channel-related), GATA-5 (transcription factor) and ER (estrogen receptor), in 106 primary gastric carcinomas by methylation-specific PCR and compared them with the past lifestyles of the patients. The methylation frequencies of the genes were 23.6, 21.7, 9.4, 32.4, 40.8 and 59.1%, respectively. Significant association was found between a decreased intake of green tea and methylation of CDX2 and BMP-2. More physical activity was correlated with a lower methylation frequency of CACNA2D3. Of these 6 genes, the methylation statuses of CDX2, BMP-2 and p16 revealed a significant interrelationship and those of CACNA2D3, GATA-5 and ER did likewise. Thus, some epidemiological factors, such as green tea intake, could be important as to determination of the methylation statuses of selected genes and may influence the development of cancer, including that of the stomach.
Follicular dendritic cells in health and disease (2012)

Follicular dendritic cells (FDCs) are unique immune cells that contribute to the regulation of humoral immune responses. These cells are located in the B-cell follicles of secondary lymphoid tissues where they trap and retain antigens (Ags) in the form of highly immunogenic immune complexes (ICs) consisting of Ag plus specific antibody (Ab) and/or complement proteins. FDCs multimerize Ags and present them polyvalently to B-cells in periodically arranged arrays that extensively crosslink the B-cell receptors for Ag (BCRs). FDC-FcγRIIB mediates IC periodicity, and FDC-Ag presentation combined with other soluble and membrane bound signals contributed by FDCs, like FDC-BAFF, -IL-6, and -C4bBP, are essential for the induction of the germinal center (GC) reaction, the maintenance of serological memory, and the remarkable ability of FDC-Ags to induce specific Ab responses in the absence of cognate T-cell help. On the other hand, FDCs play a negative role in several disease conditions including chronic inflammatory diseases, autoimmune diseases, HIV/AIDS, prion diseases, and follicular lymphomas. Compared to other accessory immune cells, FDCs have received little attention, and their functions have not been fully elucidated. This review gives an overview of FDC structure, and recapitulates our current knowledge on the immunoregulatory functions of FDCs in health and disease. A better understanding of FDCs should permit better regulation of Ab responses to suit the therapeutic manipulation of regulated and dysregulated immune responses.
ChemInform Abstract: Enantio‐ and Diastereocontrolled Dopamine D1, D2, D3, and D4 Receptor Binding of N‐(3‐Pyrrolidinylmethyl)benzamides Synthesized from Aspartic Acid. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Neuronal damage in T1-hypointense multiple sclerosis lesions demonstrated in vivo using proton magnetic resonance spectroscopy (1999)

Hypointense T1 lesions in multiple sclerosis patients correlate with axonal loss at autopsy and biopsy. We evaluated the chemical substrate of hypointense T1 lesions by using in vivo proton magnetic resonance spectroscopy, and analyzed the spectroscopic correlate of increased T1-relaxation time measurements. Localized proton magnetic resonance spectroscopy and T1-relaxation time measurements were performed in lesions, selected on T1-weighted spin-echo magnetic resonance images according to degree of hypointensity, in normal appearing white matter (NAWM) and in normal white matter of controls. In NAWM, prolongation of T1-relaxation time and a decrease in N-acetylaspartate (NAA) were present, compared with normal white matter. Severely hypointense lesions showed a lower concentration of NAA and creatine compared with NAWM and a lower concentration of NAA compared with isointense to mildly hypointense lesions. NAA concentration correlated with degree of hypointensity of lesions and with T1-relaxation time within the spectroscopic voxel. Our results provide the first in vivo evidence of axonal damage in severely hypointense T1 lesions in multiple sclerosis patients. T1-relaxation time correlates with the concentration of NAA in both multiple sclerosis lesions and NAWM, indicating that this parameter deserves further evaluation to monitor disease progression.