gebhart/patrepeval huggingface dataset:
RaS-RiPPs in Streptococci and the Human Microbiome (2022)

Radical <i>S</i>-adenosylmethionine (RaS) enzymes have quickly advanced to one of the most abundant and versatile enzyme superfamilies known. Their chemistry is predicated upon reductive homolytic cleavage of a carbon-sulfur bond in cofactor <i>S</i>-adenosylmethionine forming an oxidizing carbon-based radical, which can initiate myriad radical transformations. An emerging role for RaS enzymes is their involvement in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a natural product family that has become known as RaS-RiPPs. These metabolites are especially prevalent in human and mammalian microbiomes because the complex chemistry of RaS enzymes gives rise to correspondingly complex natural products with minimal cellular energy and genomic fingerprint, a feature that is advantageous in microbes with small, host-adapted genomes in competitive environments. Herein, we review the discovery and characterization of RaS-RiPPs from the human microbiome with a focus on streptococcal bacteria. We discuss the varied chemical modifications that RaS enzymes introduce onto their peptide substrates and the diverse natural products that they give rise to. The majority of RaS-RiPPs remain to be discovered, providing an intriguing avenue for future investigations at the intersection of metalloenzymology, chemical ecology, and the human microbiome.
COLLABORATIVERESOURCE MANAGEMENT FOR VIDEOOVER WIRELESS MULTI-HOPMESH NETWORKS (2006)

Inthis paper, weconsider theproblem ofreal-time multimedia transmission amongseveral peers(users). Thepeersusea heterogeneous wireless multi-hop meshnetwork forthedelivery of these high-bandwidth streams. Oneofthemainchallenges ofthe considered problem isthedivision ofthescarce wireless resources amongthevarious peers. Toaddress this problem, wepropose an efficient, distributed andcollaborative framework forwireless resource exchanges that enables peers todivide available wireless resources amongthemselves basedontheir quality ofservice (QoS)requirements, theunderlying channel conditions and network topology. Thescalable coding ofthevideo content and decomposition ofvideo flows intovarious sub-flows (priorities) allowpeerstotransfer thevideoatdifferent quality levels, depending onthenetwork load. Userscollaboratively decide whichoftheir sub-flows toadmit, andwhichpaths these sub-flows should betransmitted oninorder tomaximize asystem defined utility. Ourresults showthatwithusercollaboration, these distributed algorithms provide systemanduserperformance comparable toacentralized exhaustive implementation. IndexTerms-Multimedia communication
Enhanced engraftment of hematopoietic stem/progenitor cells by the transient inhibition of an adaptor protein, Lnk (2005)

Hematopoietic stem cells (HSCs) are the key elements responsible for maintaining blood-cell production throughout life and for lymphohematopoietic reconstitution following bone marrow (BM) transplantation. Enhancement of the engrafting potential and expansion capabilities of HSCs as well as hematopoietic progenitor cells (HPCs) has been a long-time desire as a means of reducing the risks and difficulties that accompany BM transplantation. The ability of HSCs/HPCs to reconstitute the hematopoietic system of irradiated hosts is negatively regulated by an intracellular adaptor protein, Lnk. Here we have identified the functional domains of Lnk and developed a dominant-negative (DN) Lnk mutant that inhibits the functions of Lnk endogenously expressed in the HSCs/HPCs and thereby potentiates the HSCs/HPCs for engraftment. Importantly, even transient expression of DN-Lnk in HSCs/HPCs facilitated their engraftment under nonmyeloablative conditions and fully reconstituted the lymphoid compartments of immunodeficient host animals. HPCs expressing DN-Lnk were efficiently trapped by immobilized vascular cell adhesion molecule-1 (VCAM-1) in a transwell migration assay, suggesting involvement of Lnk in the regulation of cell mobility or cellular interaction in microenvironments. Transient inhibition of Lnk or Lnk-mediated pathways could be a potent approach to augment engraftment of HSCs/HPCs without obvious side effects.
Overexpression of dopamine D2 receptors reduces alcohol self‐administration (2001)

The mechanism(s) underlying predisposition to alcohol abuse are poorly understood but may involve brain dopamine system(s). Here we used an adenoviral vector to deliver the dopamine D2 receptor (DRD2) gene into the nucleus accumbens of rats, previously trained to self-administer alcohol, and to assess if DRD2 levels regulated alcohol preference and intake. We show that increases in DRD2 (52%) were associated with marked reductions in alcohol preference (43%), and alcohol intake (64%) of ethanol preferring rats, which recovered as the DRD2, returned to baseline levels. In addition, this DRD2 overexpression similarly produced significant reductions in ethanol non-preferring rats, in both alcohol preference (16%) and alcohol intake (75%). This is the first evidence that overexpression of DRD2 reduces alcohol intake and suggests that high levels of DRD2 may be protective against alcohol abuse.
Coupling of DNA binding and helicase activity is mediated by a conserved loop in the MCM protein (2008)

Minichromosome maintenance (MCM) helicases are the presumptive replicative helicases, thought to separate the two strands of chromosomal DNA during replication. In archaea, the catalytic activity resides within the C-terminal region of the MCM protein. In Methanothermobacter thermautotrophicus the N-terminal portion of the protein was shown to be involved in protein multimerization and binding to single and double stranded DNA. MCM homologues from many archaeal species have highly conserved predicted amino acid similarity in a loop located between beta7 and beta8 in the N-terminal part of the molecule. This high degree of conservation suggests a functional role for the loop. Mutational analysis and biochemical characterization of the conserved residues suggest that the loop participates in communication between the N-terminal portion of the helicase and the C-terminal catalytic domain. Since similar residues are also conserved in the eukaryotic MCM proteins, the data presented here suggest a similar coupling between the N-terminal and catalytic domain of the eukaryotic enzyme.
Measurement of onset of structural relaxation in melt-quenched phase change materials (2021)

Chalcogenide phase change materials enable non-volatile, low-latency storage-class memory. They are also being explored for new forms of computing such as neuromorphic and in-memory computing. A key challenge, however, is the temporal drift in the electrical resistance of the amorphous states that encode data. Drift, caused by the spontaneous structural relaxation of the newly recreated melt-quenched amorphous phase, has consistently been observed to have a logarithmic dependence in time. Here, we show that this observation is valid only in a certain observable timescale. Using threshold-switching voltage as the measured variable, based on temperature-dependent and short timescale electrical characterization, we experimentally measure the onset of drift. This additional feature of the structural relaxation dynamics serves as a new benchmark to appraise the different classical models to explain drift.
Case Start Timing of Adult Spinal Deformity Surgeries: Does the Wait Matter? (2022)

<h3>Background</h3> Adult spinal deformity (ASD) surgery can entail complex reconstructive procedures. It is unclear whether there is any effect of case start time on outcomes. We sought to evaluate the effects of case start time and day of the week on 90-day complication, readmission, and revision rates after ASD surgery. <h3>Methods</h3> This is a retrospective study of 1040 ASD patients from a single institution. We collected start times and day of the week for cases from 2011 to 2018. Early start was designated as any case starting either before or at 7:30 am or between 7:30 and 11 am; late start was designated as any case starting at 11 am or later. Outcome measures include 90-day complication, revision, and readmission rates. <h3>Results</h3> A total of 1040 ASD patients (age, 46 ± 23 years; body mass index, 25 ± 7; American Society of Anesthesiologists classification, 2.5 ± 0.6; levels fused, 10 ± 4; three column osteotomy (3CO), 13%) were included. There was no association between surgery day of the week and length of stay, 90-day complication, readmission, or reoperation rates in the adjusted analyses. Late start cases had higher rates of 90-day readmission (10.5% vs 6.0%, <i>P</i> = 0.02), reoperation (11.9% vs 6.6%, <i>P</i> = 0.008), and neurologic injury (5.2% vs 2.1%, <i>P</i> = 0.019). Subanalysis of neurologic complications demonstrated that there was a higher rate of postoperative radiculopathy (<i>P</i> = 0.007) and residual central or foraminal stenosis (<i>P</i> = 0.029) in late start cases. A late start time was predictive of increased risk for 90-day readmission (OR 1.8, <i>P</i> = 0.02), unplanned reoperation (OR 1.9, <i>P</i> = 0.009), and neurologic complication (OR 2.1, <i>P</i> = 0.046). <h3>Conclusions</h3> A late OR start time was predictive of increased risk for neurologic complication, 90-day readmission, and unplanned reoperation. The well-established protocols for first start OR times for elective ASD surgery may decrease outcome risk and reduce variability in complication rates. <h3>Clinical Relevance</h3> Understanding the impact of start time on outcomes and complications after ASD surgery is helpful for surgeons in preoperative planning and for institutions and hospitals’ allocation of operating room staff and resources. <h3>Level of Evidence</h3> 3.
Regional Systems of Care to Optimize Timeliness of Reperfusion Therapy for ST-Elevation Myocardial Infarction (2007)

The Mayo Clinic ST-elevation myocardial infarction protocol demonstrates the feasibility of implementing strategies to optimize the timeliness of reperfusion therapy and the times that can be achieved through coordinated systems of care for ST-elevation myocardial infarction patients presenting to a PCI center (Saint Marys Hospital) and 28 regional hospitals without PCI capability located up to 150 miles away across 3 states.
Simulating the Permeability Reduction due to Asphaltene Deposition in Porous Media (2009)

Abstract A static to dynamic approach to modeling Asphaltenes has been developed and validated. A new algorithm for static asphaltene modeling uses a multi-solid thermodynamics approach where the equality of fugacity for each component and phase is applied at equilibrium conditions. This is required for minimizing the Gibbs free energy. The fractal distribution function used for the splitting and characterization of heavy components provides accurate results. The precipitation and re-dissolution of asphaltenes are investigated for a relatively heavy crude oil from an Iranian field. A series of experiments are designed and conducte quantitatively to obtain the permeability reduction in a slim tube. Using a dynamic reservoir simulator, a 3-dimensional asphaltene model is developed to simulate the precipitation, flocculation, deposition and its impact on permeability in a slim tube. With this approach, the asphaltene is defined as a set of component(s) that can precipitate depending on their molar percentage weight in solution. The simulated permeability reduction due to asphaltene deposition shows good agreement with our experimental data. 1. Introduction Asphaltenes can reduce the hydrocarbon effective mobility by:a) Blocking pore throats thus reducing the rock permeability.b) Adsorbing onto the rock and altering the formation wettability from water-wet to oil-wet, hence diminishing the effective permeability to oil and increasing the irreducible oil saturation.c) Increasing the reservoir fluid viscosity by forming a colloidal solution in the oil phase. The most frequently encountered scenario of asphaltene-induced formation damage is when under saturated oil is being produced without water. The most dominant damage mechanism is blockage of pore throats by asphaltene precipitation and thus causing a reduction in rock permeability. In comparison most wax-related formation damage is caused by cooling due to excessive draw down across the perforations or due to hot oiling operations or organic solids entering the formation due to overbalance conditions. In all cases, the damage area is restricted to the wellbore zone (several inches to 1 feet). In the case of asphaltenes, the formation damage may occur many feet from the wellbore depending on the drawdown [1,2]. Several authors have studied different models for asphaltene deposition in core tests. Civan et al. [3, 4] assumed that the flow channels in porous media are grouped into plugging and non-plugging pathways, and for the deposition model they use surface adsorption, pore throat plugging, and entrainment of deposits. Ali and Islam [5] assumed that Asphaltene is suspended in crude oil and ready to deposit, and for the deposition model they consider surface adsorption and entrainment of deposits. Wang et al. [6,7] considered asphaltene precipitation could be simulated by ideal solution theory, and for the deposition model they used surface adsorption, plugging, and entrainment.
Concurrent chronic lymphocytic leukemia/small lymphocytic lymphoma and hairy cell leukemia: clinical, pathologic and molecular features (2020)

Simultaneous occurrence of hairy cell leukemia (HCL) and chronic lymphocytic leukemia/small lymphocytic lymphoma (termed CLL) is very rare. Clinical characteristics, pathology and management of these cases have not been well described. We present six patients with CLL and HCL or HCL variant (HCL-v). Of six patients, three were initially diagnosed with CLL and later developed concurrent HCL. Two patients had concurrent HCL or HCL-v and CLL at initial diagnosis. One had HCL first, followed by concurrent CLL. Polymerase chain reaction analysis demonstrated B-cell clonality in all cases, with two distinct clonal populations in four cases, and three clonal populations in one case. Five patients were treated with a combination of a purine analog such as fludarabine, cladribine, and pentostastin with either rituximab or ibrutinib, while one received dabrefenib and trametinib. All patients achieved a durable response to either CLL or HCL-directed therapy with reduction or ablation of coexisting B-cell clones.
Novel Hybrid Bonding Technology Using Ultra-High Density Cu Nano-Pillar for Exascale 2.5D/3D Integration (2015)

We propose a novel hybrid bonding technology with a high stacking yield using ultra-high density Cu nanopillar (CNP) for exascale 2.5D/3D integration. To solve the critical issues of a current standard hybrid bonding technology, we developed scaled electrodes with slightly extruded structure and unique adhesive layer of anisotropic conductive film composed of ultra-high density CNP. Test element group (TEG) dies with 7-mm × 23-mm size are bonded to interposer wafer by a new hybrid bonding technology. Scaled electrodes with 3-μm diameter and 6-μm pitch are formed in each TEG chip. We confirmed for the first time that a huge number of electrodes of 4309200 are successfully connected in series with the joining yield of 100% due to the ultra-high density CNP.
Factors Influencing Circadian Rhythms in Acetaminophen Lethality (1984)

Experiments were conducted to examine the effects of changes in lighting schedules and food consumption on circadian rhythms in acetaminophen lethality and hepatic glutathione levels in male mice. Under a normal lighting schedule (light: 06.00-18.00 h), male mice exhibited a circadian rhythm in acetaminophen lethality (peak: 18.00 h; nadir: 06.00, 10.00 h) and an inverse rhythm in hepatic glutathione concentrations (peak: 06.00, 10.00 h; nadir: 18.00 h). Under a reversed lighting schedule (light: 18.00-06.00 h) the glutathione rhythm was reversed and the rhythm in acetaminophen lethality was altered showing greater sensitivity to the drug. Under continuous light, there was a shift in the acetaminophen lethality and the hepatic glutathione rhythms. Under continuous dark, both rhythms were abolished. Under a normal lighting regimen, hepatic glutathione levels were closely correlated with food consumption; i.e., both were increased during the dark phase and decreased during the light phase. Fasting the mice for 12 h abolished the rhythms in acetaminophen lethality and hepatic glutathione levels; moreover, the lethality was increased and the hepatic glutathione levels were decreased. These experiments show that both lighting schedules and feeding can alter the circadian rhythms in acetaminophen lethality and hepatic glutathione levels in male mice.
A randomized, controlled trial to assess a novel colorectal cancer screening strategy: the conversion strategy. A comparison of sequential sigmoidoscopy and colonoscopy with immediate conversion from sigmoidoscopy to colonoscopy in patients with an abnormal screening sigmoidoscopy (2000)

Our study was a randomized, controlled trial to assess a novel strategy that provides comprehensive colorectal cancer screening in a single visit versus traditional sigmoidoscopy and, where appropriate, colonoscopy on a subsequent day. METHODS : Consecutive patients referred for screening were randomized to control or so-called “conversion” groups. Patients in the control group were prepared for sigmoidoscopy with oral phospho-soda. Those with an abnormal sigmoidoscopy were scheduled for colonoscopy on a future day after oral polyethylene glycol preparation. In the conversion group, patients were prepared with oral phospho-soda. Patients with a polyp >5 mm or multiple diminutive polyps were converted from sigmoidoscopy to colonoscopy, allowing comprehensive screening in a single visit. Clinical outcomes were assessed by postprocedure physician and patient questionnaires. RESULTS : Two hundred thirty-five patients were randomized (control = 121, conversion = 114). In the control group, 28% had an indication for colonoscopy. Three of 33 (9%) with an abnormal sigmoidoscopy did not return for colonoscopy. At colonoscopy, 27% had a proximal adenoma. In the conversion group, 28% had an abnormal sigmoidoscopy and underwent conversion to colonoscopy. Forty-one percent undergoing colonoscopy in the conversion group had a proximal adenoma. Physicians reported no differences in preparation or procedure difficulty, whereas patients reported no differences in the level of comfort or overall satisfaction between groups. When queried regarding preferences for future screening, 96% chose the conversion strategy. CONCLUSIONS : The conversion strategy led to similar outcomes compared to traditional screening while improving compliance with colonoscopy in patients with an abnormal sigmoidoscopy.
CCR10 expression is required for immunogenicity of a HIV-1env DNA vaccine encoding CCL28 to enhance HIV-1env-specific IgG and IgA at relevant mucosal sites (VAC7P.986) (2014)

Abstract Development of a vaccine that drives anti-viral mucosal B cell responses is critical for protection against HIV-1 infection. It is currently unknown whether triggering CCR10/CCL28 pathways in a DNA-based vaccine results in induction of HIV-1env specific B cell immunity at mucosal sites of infection. We hypothesized that co-immunization with HIV-1env/CCL28 molecular adjuvant would augment B cell responses at gastrointestinal and vaginal sites and require CCR10. CCL28 co-immunized WT mice displayed a significant enhancement of HIV-1env specific antibody titers in serum, feces and vaginal washes, and enhanced HIV-1 specific IgA responses were abrogated in CCR10KO mice. CCL28 co-immunization did not increase the breadth of linear B cell epitopes in WT mice, but augmented the dominant epitopes elicited by antigen immunization alone. The frequency of splenic and intestinal IgA+CD19+B220+CD138+CCR10+ plasmablasts was augmented in the CCL28 co-immunized WT mice over antigen-only immunized WT controls. The physiological relevance of these findings was confirmed in a NHP model of intravaginal SIVsmE660 challenge in which CCL28 co-immunization resulted in significant increases in serum/vaginal IgG/IgA, decrease in peak viral loads, significant suppression of viral titers over 120 days, and recovery of CD4 T cells. These data support a role for CCL28 in targeting protective anti-viral B cells to mucosal sites when delivered as molecular adjuvants for HIV-1env DNA-based vaccines.
Early Development of Time-Resolved Volumetric Doppler Velocimetry for New Insights in Hot Supersonic Jet Noise (2012)

The early development of a novel implementation of Doppler-based flow velocimetry, termed the time-resolved volumetric Doppler velocimetry (TRVDV) technique, is discussed for the specific application of kinematics measurements related to flow-generated noise in hot supersonic jets. By combining new detector technologies with unique uses of advanced laser-based photonics, TRVDV promises to produce many hundreds of velocity vectors distributed throughout volumes of the flow at 100kHz repetition rates over long contiguous durations—information needed in real flows to quantitatively evaluate noise sources. Herein, we describe the instrument currently under development and present some single-point velocity statistics and signals from a two-point prototype instrument in a cold supersonic jet. Spectral analysis for the stream-wise normal stress has been done for the single-point data at the center of the jet near the exit plane via slot correlation, with results out to approximatlely 400kHz presented. Initial results for measuring two points spaced along the collection optics axis exhibit the key attribute required for obtaining volumetric results with the system, namely, sufficient scattering intensity with varying depth of focus. Future development of the instrumentation system for many point measurements are discussed in light of current results. It is planned that the mature TRVDV package will be portable such that the system may be shipped to larger facilities for aeroacoustics experiments with results at levels of detail never before obtained.
Time Series Analysis With Application to Velocity Fluctuation Data Measured in a Wind Tunnel, Atmospheric Boundary Layer (1994)

The techniques used to estimate the statistical parameters describing the&#13;\nturbulent velocity fluctuations in an urban atmospheric boundary layer simulated&#13;\nin a long test section wind tunnel are described. An extensive review of the&#13;\ntheory underlying the selection of autocovariance and spectral density function&#13;\nestimators and of the equations needed for the digital evaluation of sample&#13;\nspectra using Fast Fourier Transforms is presented. A computer program for&#13;\nevaluation of sample spectra and autocovariances, developed on the basis of these&#13;\nequations and including the determination of confidence intervals for the&#13;\nspectral estimates, is given. The selection of series and subseries lengths and&#13;\nsampling intervals is illustrated through application of the program to&#13;\nautoregressive processes and to the atmospheric boundary layer velocity&#13;\nfluctuation data. The determination of integral length scales and the scales in&#13;\nthe inertial subrange of the spectrum is discussed in particular for the velocity&#13;\nfluctuation data.
Lean Management in der Kleinserienfertigung (2012)

Kurzfassung In diesem Beitrag wird die Anwendbarkeit von Lean Management-Methoden in der Kleinserienfertigung diskutiert. Es werden dabei unterschiedliche Methoden und Methoden-Kombinationen des Lean Managements untersucht. Der Anwendungsgegenstand ist die Produktion von Windkrafttürmen. Hierfür sind die Zielkriterien Durchlaufzeit, Auslastung, Termintreue und Flexibilität untersucht worden. Die Bewertung der Methoden zeigt, dass hauptsächlich Methoden-Kombinationen gute Resultate erzielen.