gebhart/patrepeval huggingface dataset:
Interplay between 4-Hydroxy-3-Methyl-2-Alkylquinoline and N-Acyl-Homoserine Lactone Signaling in a Burkholderia cepacia Complex Clinical Strain (2017)

Species from the <i>Burkholderia cepacia</i> complex (Bcc) share a canonical LuxI/LuxR quorum sensing (QS) regulation system named CepI/CepR, which mainly relies on the acyl-homoserine lactone (AHL), octanoyl-homoserine lactone (C<sub>8</sub>-HSL) as signaling molecule. <i>Burkholderia ambifaria</i> is one of the least virulent Bcc species, more often isolated from rhizospheres where it exerts a plant growth-promoting activity. However, clinical strains of <i>B. ambifaria</i> display distinct features, such as phase variation and higher virulence properties. Notably, we previously reported that under laboratory conditions, only clinical strains of the <i>B. ambifaria</i> species produced 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs) <i>via</i> expression of the <i>hmqABCDEFG</i> operon. HMAQs are the methylated counterparts of the 4-hydroxy-2-alkylquinolines (HAQs) produced by the opportunistic human pathogen <i>Pseudomonas aeruginosa</i>, in which they globally contribute to the bacterial virulence and survival. We have found that unlike <i>P. aeruginosa</i>'s HAQs, HMAQs do not induce their own production. However, they indirectly regulate the expression of the <i>hmqABCDEFG</i> operon. In <i>B. ambifaria</i>, a strong link between CepI/CepR-based QS and HMAQs is proposed, as we have previously reported an increased production of C<sub>8</sub>-HSL in HMAQ-negative mutants. Here, we report the identification of all AHLs produced by the clinical <i>B. ambifaria</i> strain HSJ1, namely C<sub>6</sub>-HSL, C<sub>8</sub>-HSL, C<sub>10</sub>-HSL, 3OHC<sub>8</sub>-HSL, 3OHC<sub>10</sub>-HSL, and 3OHC<sub>12</sub>-HSL. Production of significant levels of hydroxylated AHLs prompted the identification of a second complete LuxI/LuxR-type QS system relying on 3OHC<sub>10</sub>-HSL and 3OHC<sub>12</sub>-HSL, that we have named CepI2/CepR2. The connection between these two QS systems and the <i>hmqABCDEFG</i> operon, responsible for HMAQs biosynthesis, was investigated. The CepI/CepR system strongly induced the operon, while the second system appears moderately involved. On the other hand, a HMAQ-negative mutant overproduces AHLs from both QS systems. Even if HMAQs are not classical QS signals, their effect on AHL-based QS system still gives them a part to play in the QS circuitry in <i>B. ambifaria</i> and thus, on regulation of various phenotypes.
An empirical model relating the auroral geomagnetic activity to the interplanetary magnetic field (1993)

A damped linear oscillator (LRC circuit) predicts a significant amount of the AL index variations when it is driven by the IMF's B South component. The model parameters are determined from fitting the AL time series and show a small, apparently nonsystematic variation with the activity level. Following an isolated external disturbance the LRC model's response peaks at 15 min ‐ 0.5 h and decays after 1–2 more hours. The time scales and the correlation between observed AL and the circuit output (60–80%) are in good agreement with earlier linear prediction filter results. The results support the modeling of the global magnetospheric behavior with dynamical systems of a few degrees of freedom.
ChemInform Abstract: Alkyne Activation with Broensted Acids, Iodine, or Gold Complexes, and Its Fate Leading to Synthetic Application (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Dynamics of the Transition from Spiral Rainbands to a Secondary Eyewall in Hurricane Earl (2010) (2018)

Abstract Airborne Doppler radar captured the inner core of Hurricane Earl during the early stages of secondary eyewall formation (SEF), providing needed insight into the SEF dynamics. An organized rainband complex outside of the primary eyewall transitioned into an axisymmetric secondary eyewall containing a low-level tangential wind maximum. During this transition, the downshear-left quadrant of the storm exhibited several notable features. A mesoscale descending inflow (MDI) jet persistently occurred across broad stretches of stratiform precipitation in a pattern similar to previous studies. This negatively buoyant jet traveled radially inward and descended into the boundary layer. Farther inward, enhanced low-level inflow and intense updrafts appeared. The updraft adjacent to the MDI was likely triggered by a region of convergence and upward acceleration (induced by the negatively buoyant MDI) entering the high-θe boundary layer. This updraft and the MDI in the downshear-left quadrant accelerated the tangential winds in a radial range where the axisymmetric wind maximum of the secondary eyewall soon developed. This same quadrant eventually exhibited the strongest overturning circulation and wind maximum of the forming secondary eyewall. Given these features occurring in succession in the downshear-left quadrant, we hypothesize that the MDI plays a significant dynamical role in SEF. The MDI within a mature rainband complex persistently perturbs the boundary layer, which locally forces enhanced convection and tangential winds. These perturbations provide steady low-level forcing that projects strongly onto the axisymmetric field, and forges the way for secondary eyewall development via one of several SEF theories that invoke axisymmetric dynamical processes.
Optimal Clustering with Missing Values (2019)

Abstract Background Missing values frequently arise in modern biomedical studies due to various reasons, including missing tests or complex profiling technologies for different omics measurements. Missing values can complicate the application of clustering algorithms, whose goals are to group points based on some similarity criterion. A common practice for dealing with missing values in the context of clustering is to first impute the missing values, and then apply the clustering algorithm on the completed data. Results We consider missing values in the context of optimal clustering, which finds an optimal clustering operator with reference to an underlying random labeled point process (RLPP). We show how the missing-value problem fits neatly into the overall framework of optimal clustering by incorporating the missing value mechanism into the random labeled point process and then marginalizing out the missing-value process. In particular, we demonstrate the proposed framework for the Gaussian model with arbitrary covariance structures. Comprehensive experimental studies on both synthetic and real-world RNA-seq data show the superior performance of the proposed optimal clustering with missing values when compared to various clustering approaches. Conclusion Optimal clustering with missing values obviates the need for imputation-based pre-processing of the data, while at the same time possessing smaller clustering errors.
193-nm haze contamination: a close relationship between mask and its environment (2003)

The integration of 193nm Lithography is close to full production for the 90nm node technology. With the potential of emerging 193nm lithographic resolution down to 65nm, the quality of 193nm reticles including binary, EAPSM and AAPSM must be outstanding so that low K1 factor reticles may be used in production. One area of concern in the IC industry is haze contamination on the mask once the reticle has been exposed to ArF radiation. In this study, haze was found outside of the pellicle and on the quartz side of the mask. Standard through-pell inspections will typically miss the contamination, yet its severity can ultimately affect mask transmission. For this reason, DuPont Photomasks and Cypress joined forces to quickly decipher how it develops. In this investigation, tests were devised which altered conditions such as mask environment, exposure, traditional and advanced cleaning chemistry. This paper describes the relationship between surface and environmental photochemical reactions, the resultant growth, analysis, and how it is controlled.
In vitro Activity of Bcr-Abl Inhibitors AMN107 and BMS-354825 against Clinically Relevant Imatinib-Resistant Abl Kinase Domain Mutants (2005)

Imatinib, a Bcr-Abl tyrosine kinase inhibitor, is a highly effective therapy for patients with chronic myelogenous leukemia (CML). Despite durable responses in most chronic phase patients, relapses have been observed and are much more prevalent in patients with advanced disease. The most common mechanism of acquired imatinib resistance has been traced to Bcr-Abl kinase domain mutations with decreased imatinib sensitivity. Thus, alternate Bcr-Abl kinase inhibitors that have activity against imatinib-resistant mutants would be useful for patients who relapse on imatinib therapy. Two such Bcr-Abl inhibitors are currently being evaluated in clinical trials: the improved potency, selective Abl inhibitor AMN107 and the highly potent dual Src/Abl inhibitor BMS-354825. In the current article, we compared imatinib, AMN107, and BMS-354825 in cellular and biochemical assays against a panel of 16 kinase domain mutants representing >90% of clinical isolates. We report that AMN107 and BMS-354825 are 20-fold and 325-fold more potent than imatinib against cells expressing wild-type Bcr-Abl and that similar improvements are maintained for all imatinib-resistant mutants tested, with the exception of T315I. Thus, both inhibitors hold promise for treating imatinib-refractory CML.
Atrial deformation: the key to maintenance of sinus rhythm in patients with atrial fibrillation? (2008)

Atrial fibrillation (AF) is the most common serious arrhythmia encountered in clinical practice, and accounts for approximately one-third of all hospitalizations for cardiac rhythm disturbances.1 Consequently, effective therapies for conversion of AF to, and maintenance of, sinus rhythm (SR) have been actively sought. Currently, catheter-based ablation techniques have been shown to be promising in the elimination of AF. However, a significant percentage of patients undergoing catheter ablation have recurrence of AF; in one recent study, only 64% of patients with paroxysmal and 45% of patients with persistent AF were AF-free at 12 months follow-up.2 Other groups have shown that with complete pulmonary vein and posterior left atrial (LA) isolation, up to 63% of chronic AF patients maintained SR at 2 years3. Therefore, there is a great interest in markers, either clinical, biological. or imaging-based, that can predict which patients will maintain SR after catheter ablation and which will revert back to AF.

Schneider and colleagues measured tissue Doppler-based strain and strain rate—measures of the degree and rate of LA deformation, respectively—24 h before, 24 h after, and 3 months post-catheter based ablation in 118 patients with either persistent or paroxysmal AF.4 Using catheter-based pulmonary vein isolation employong a ‘double Lasso’ technique, SR was achieved immediately following the procedure in all patients. Of the 118 patients followed-up for a 3-month period after catheter ablation a total of 82 patients (69%) … 

*Corresponding author. Tel: +1 713 798 2608, Fax: +1 713 798 2751, Email: hishamd{at}bcm.edu
Surgical Management of Stress Urinary Incontinence (2004)

*Section of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, and †Center for Female Pelvic Medicine and Reconstructive Surgery, The Cleveland Clinic Foundation, Cleveland, Ohio Correspondence: Mark D. Walters, MD, Cleveland Clinic Foundation, Department of Obstetrics and Gynecology, Desk A-81, 9500 Euclid Avenue, Cleveland, OH 44195. E-mail:[email protected]
Excited state management (2023)

Arrangements and techniques for providing organic emissive layers are provided, in which the emissive layer includes a first dopant having a dissociative energy level. A second dopant in the emissive layer provides a solid state sink energy level, to which doubly excited excitons and/or polarons may transition instead of to the dissociative energy level, thereby decreasing the undesirable effects of transitions to the dissociative energy level.
Iodine Frequency Reference on a Sounding Rocket (2019)

The development of compact optical frequency references plays an important role in future optical timing systems, on the ground and in space, including next-generation global-navigation satellite systems. Realization and qualification of such systems is held back by technical challenges in creating robust, reliable devices for optical metrology under demanding conditions. Here researchers demonstrate the autonomous operation of an I${}_{2}$ frequency reference and the measurement of its optical frequency using a dual frequency comb on a sounding rocket, as a milestone on the way to routine application of such optical technologies in space.
B-scan ultrasonographic monitoring of orthotopic xenografted plexiform neurofibroma in mice. (2014)

High frequency sonographic measurement is a superior non-invasive method for monitoring small grafts of slowly growing benign tumours in mice in vivo, e.g. plexiform neurofibroma, and is especially suitable for tracing the effects of drugs at multiple time-points, thus allowing a very cost-effective follow-up.
Matrix metallopeptidase 9 targeted by hsa‐miR‐494 promotes silybin‐inhibited osteosarcoma (2017)

Osteosarcoma (OS) is the most common malignant tumor that develops in bone. Its mortality is very high. Therefore, study of mechanisms of pathogenesis of the OS is urgently required. Previous studies of microarray showed that the expression levels of matrix metallopeptidase 9 (MMP-9) altered significantly in OS. In addition, overexpression of MMP-9 is recognized as an indicator in cancer. However, the exact roles of MMP-9 in OS are not fully investigated. Thus, we firstly studied the roles of MMP-9 in OS and revealed that silence of MMP-9 inhibited OS cell proliferation as determined by MTT assay and colony formation assay. Secondly, we conducted TUNEL assay and confirmed loss of functions of MMP-9 induced OS cell apoptosis. Next, we used lentivector packaging method to overexpress MMP-9 and found that overexpression of MMP-9 promoted OS cell migration. Fourthly, the results of luciferase assay showed that MMP-9 was targeted by hsa-miR-494, which inhibited OS. Fifthly, we revealed that the levels of hsa-miR-494 were upregulated by the drug silybin which inhibited OS. Finally, we revealed that silybin inhibited OS cell viability by altering the protein levels of β-catenin and Runt-related transcription factor 2 (RUNX2) as determined by western blot and immunocytochemistry (ICC).
Multi-Band Filter Built with a Periodically Patterned Stripline (2012)

A novel unit cell consisting of a meander shaped metallic patch, positioned in between two dielectric grounded layers and connected to one of them by three vias is proposed. The large number of reactive elements composing the structure are shown to determine an equally large number of electromagnetic band-gaps making the structure appropriate for advanced sensor or multi-band filtering applications in modern wireless systems. Parametric studies considering the value of the dielectric constant of one of the dielectric layers, for two orthogonal directions of propagation are reported.
A State-Of-The-Art Review of Cloud Forensics (2014)

Cloud computing and digital forensics are emerging fields of technology. Unlike traditional digital forensics where the target environment can be almost completely isolated, acquired and can be under the investigators control; in cloud environments, the distribution of computation and storage poses unique and complex challenges to the investigators. Recently, the term “cloud forensics” has an increasing presence in the field of digital forensics. In this state-of-the-art review, we included the most recent research efforts that used “cloud forensics” as a keyword and then classify the literature into three dimensions: (1) survey-based, (2) technology-based and (3) forensics-procedural-based. We discuss widely accepted standard bodies and their efforts to address the current trend of cloud forensics. Our aim is not only to reference related work based on the discussed dimensions, but also to analyse them and generate a mind map that will help in identifying research gaps. Finally, we summarize existing digital forensics tools and the available simulation environments that can be used for evidence acquisition, examination and cloud forensics test purposes.
Screening for Atrial Fibrillation in American Indian Adults in a Tribal Primary Care Clinic (2021)

Background American Indian adults have a higher risk of atrial fibrillation (AF) compared with other racial groups. We implemented opportunistic screening to detect silent AF in American Indian adults attending a tribal health system using a mobile, single-lead ECG device. Methods and Results American Indian patients aged ≥50 years followed in a tribal primary care clinic with no history of AF underwent a 30-second ECG. A cardiologist overread all tracings to confirm the diagnosis of AF. After AF was confirmed, patients were referred to their primary care physician for initiation of anticoagulation. Patients seen over the same time period, who were not undergoing screening, served as controls. A total of 1019 patients received AF screening (mean age, 61.5±8.9 years, 62% women). Age and sex distribution of those screened was similar to the overall clinic population. New AF was diagnosed in 15 of 1019 (1.5%) patients screened versus 4 of 1267 (0.3%) patients who were not screened (mean difference, 1.2%; 95% CI, 0.3%-2.2%, <i>P</i>=0.002). Eight of 15 with new screen-detected AF were aged <65 years. Those with screen-detected AF were slightly older and had a higher CHA<sub>2</sub>DS<sub>2</sub>-VASc score than those without AF. Fourteen of 15 patients diagnosed with new AF had a CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥1 and initiated anticoagulation. Conclusions Opportunistic, mobile single-lead ECG screening for AF is feasible in tribal clinics, and detects more AF than usual care, leading to appropriate initiation of anticoagulation. AF develops at a younger age in American Indian adults who would likely benefit from earlier AF screening. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT03740477.
ADAMTS13 Substrate Recognition of von Willebrand Factor A2 Domain (2005)

ADAMTS13 controls the multimeric size of circulating von Willebrand factor (VWF) by cleaving the Tyr1605-Met1606 bond in theA2 domain. To examine substrate recognition, we expressed in bacteria and purified three A2 (VWF76-(1593-1668), VWF115-(1554-1668), VWFA2-(1473-1668)) and one A2-A3 (VWF115-A3-(1554-1874)) domain fragments. Using high pressure liquid chromatography analysis, the initial rates of VWF115 cleavage by ADAMTS13 at different substrate concentrations were determined, and from this the kinetic constants were derived (Km 1.61 microM; kcat 0.14 s(-1)), from which the specificity constant kcat/Km was calculated, 8.70 x 10(4) m(-1) s(-1). Similar values of the specificity constant were obtained for VWF76 and VWF115-A3. To identify residues important for recognition and proteolysis of VWF115, we introduced certain type 2A von Willebrand disease mutations by site-directed mutagenesis. Although most were cleaved normally, one (D1614G) was cleaved approximately 8-fold slower. Mutagenesis of additional charged residues predicted to be in close proximity to Asp1614 on the surface of the A2 domain (R1583A, D1587A, D1614A, E1615A, K1617A, E1638A, E1640A) revealed up to 13-fold reduction in kcat/Km for D1587A, D1614A, E1615A, and K1617A mutants. When introduced into the intact VWFA2 domain, proteolysis of the D1587A, D1614A, and E1615A mutants was also slowed, particularly in the presence of urea. Surface plasmon resonance demonstrated appreciable reduction in binding affinity between ADAMTS13 and VWF115 mutants (KD up to approximately 1.3 microM), compared with VWF115 (KD 20 nM). These results demonstrate an important role for Asp1614 and surrounding charged residues in the binding and cleavage of the VWFA2 domain by ADAMTS13.
An Emerging Cardiovascular Disease: Takotsubo Syndrome (2019)

Takotsubo syndrome (TTS) is a recently identified cardiac disease, which is far from being completely known. The aims of this narrative review are to provide a better understanding of the pathophysiological features of TTS and to update clinical findings in order to improve the management of subjects affected by this syndrome (according to the most recent consensus papers issued by the international scientific societies). We based our search on the material obtained via PubMed up to April 2019. The terms used were "Takotsubo Syndrome and Takotsubo cardiomyopathy" in combination with "heart failure, pathophysiology, complications, diagnosis, and treatment." TTS is a reversible form of ventricular dysfunction usually characterized by akinesia of the apex in the absence of obstructive coronary artery disease. In its initial phase, TTS may be indistinguishable from AMI and is usually triggered by a sudden emotional/physical stressor which abruptly increases catecholamine levels. However, the mechanisms by which catecholamines or other unidentified molecules can cause myocardial dysfunction is unknown. In-hospital stay may be hampered by various life-threatening complications, while data on long-term survival remain scarce and unclear. Furthermore, TTS may sometimes recur. We believe that TTS is clearly a much more complex condition than previously thought. Much remains to be discovered about its pathophysiologic mechanisms, the role of the link between the heart and brain and that of triggering factors and gender, and the reasons why this syndrome displays different phenotypes and sometimes recurs. Undoubtedly, preliminary evidence from pathophysiological studies (mainly genetic studies) has shown promising advances. However, prospective randomized clinical trials are still needed in order to identify and to tailor the best medical treatments for TTS patients.
5.1: High Information Content Display Based on Reflective LC on Silicon Light Valves (1998)

Abstract A projection display has been developed based on reflective, liquid crystal light valves fabricated on a crystalline silicon active matrix array. The light valves utilize the 45 degree twisted nematic LC mode. The optical system is based on dichroic mirror color separation, three polarizing beam splitters and a dichroic color combining cube. The display has native SXGA or UXGA resolution with full multisync capability for other formats and provides 600 ANSI lumens with 100:1 ANSI contrast.
Cyclazocine and methadone in narcotic addiction (1967)

Narcotic addicts volunteered for treatment with methadone hydrochloride and cyclazocine in a community hospital. Eight of 15 addicts treated with methadone have been maintained in the community for more than one year, and their continued contact with the clinic provided a basis for habilitation. Cyclazocine, an experimental narcotic antagonist, was given to 103 patients. In 51, in a prolonged hospitalization "therapeutic community" program, cyclazocine did not augment their treatment. But, cyclazocine was successful in 52 additional patients treated rapidly and hospitalized for less than two months. After discharge, thirty-one attended a clinic three times weekly for two months. Four to 5 mg cyclazocine daily effectively blocked 15 mg intravenous heroin, up to 28 hours. Secondary effects of increased libido, euphoria, constipation, restlessness, and insomnia abated within two weeks. These results are promising, and cyclazocine is worthy of further investigation.