gebhart/patrepeval huggingface dataset:
Mining the human gut microbiome identifies mycobacterial d-arabinan degrading enzymes (2022)

Abstract Division and degradation of bacterial cell walls requires coordinated action of a myriad of enzymes. This particularly applies to the elaborate cell walls of acid-fast organisms such as Mycobacterium tuberculosis , which consist of a multi-layered cell wall that contains an unusual glycan called arabinogalactan. Enzymes that cleave the d -arabinan core of this structure have not previously been identified in any organism. We have interrogated the diverse carbohydrate degrading enzymes expressed by the human gut microbiota and uncovered four families of glycoside hydrolases with the capability to degrade the d -arabinan or d -galactan components of arabinogalactan. Using novel exo- d -galactofuranosidases from gut bacteria we generated enriched d -arabinan and used it to identify D. gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan. We have identified new members of the DUF2961 family (GH172), and a novel family of glycoside hydrolases (DUF4185) that display endo- d -arabinofuranase activity. The DUF4185 enzymes are conserved in mycobacteria and found in many microbes, suggesting that the ability to degrade mycobacterial glycans plays an important role in the biology of diverse organisms. All mycobacteria encode two conserved endo- d -arabinanases that display different preferences for the d -arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.
An engineering methodology for kite design (2011)

Kites have seen substantial development in the last 10 years, going from mostly toys to high-performance sports-related equipment for e.g. kite surfing. The design process of these kites, however, is mostly a trial-and-error affair. Ten years after the sports-related kite revolution a new development is is emerging: Industrial applications for kites. Systems to propel ships and generate sustainable energy are now under development worldwide at over 40 companies and institutes. These new industrial applications will put strickter and more complex requirements on these kites. The current trial-and-error approach to the design of kites will not suffice. In this thesis a different design methodology is proposed. This methodology leans on three pillars. The first pillar is "Knowledge". As it turns out, there is still a lot unknown about the behavior of kites. This thesis further develops that knowledge. The seccond pillar is "Simulation". Nowadays, a large number of prototypes are produced and tested. So many in fact, that many designers do not even have the time to test them all. With the advance of complex industrial kites, this situation is expected to escalate. The capability of virtually testing kites will shrink the prototype phase into more managable proportions. Furthermore, it will contribute to the understanding of kites as well. This thesis proposes a number of models to simulate kites on a conventional desktop computer. These models include both rigid-body and multi-body models. The latter is capable of simulating a kite including its extreme flexibility. The third and last pillar is "Measurement". Controlled and reproducable measurements are essential for validation and evaluation. The thesis closes with a number of case studies which show the advantages and opportunities of this methodology.
Re: Response to Referee #1: Comparative Analysis of MODIS, MISR and AERONET Climatology over the Middle East and North Africa (2018)

The author presents an analysis of collocated MISR and MODIS satellite AOD retrieval data over seven AERONET sites for a 16-year period. These sites are located in or next to the desert regions of North Africa and the Middle C1
State of the Art in Anomaly Detection and Reaction (1999)

This paper presents a view of the state of the art in anomaly detection and reaction (ADR) technology. The paper develops the view from six sources: three prior reports (two national, one MITRE), a survey of commercially available software, a survey of government software, and a survey of government-funded research projects. ADR encompasses the automated capabilities that can detect or find anomalies in computer systems, report them in useful ways, remove discovered anomalies, and repair damage they may have caused. Included in this scope of interest are traditional intrusion detection and reaction tools. The broader scope of anomaly detection and reaction also includes vulnerability scanners, infraction scanners, and security compliance monitors. These tools protect not only against intruders but against errors and carelessness in administration and operation of end systems and network components. This synopsis draws on the following sources of information: (1) the National Info-Sec Technical Baseline report on intrusion detection and response; (2) the description of the state of the art in network-based intrusion detection systems in a report of Hill and Aguirre; (3) the report of the Intrusion Detection Subgroup of the National Security Telecommunications Advisory Committee on the implications of intrusion detection technology research and development on national security and emergency preparedness; (4) product descriptions of commercial off-the-shelf (COTS) and government off-the-shelf (GOTS) ADR systems; and (5) descriptions of current research in anomaly detection and reaction. Tables show intrusion detection tools by product type and architecture, provide commentary on issues in ADR, present the main thrust of numerous research efforts in ADR, and provide a condensation of the state of the art in ADR.
Accurate flow cytometric membrane potential measurement in bacteria using diethyloxacarbocyanine and a ratiometric technique (1999)

The ratiometric technique for MP estimation using DiOC2(3) is substantially more accurate and precise than those previously available, and may be useful in studies of bacterial physiology and in investigations of the effects of antibiotics and other agents on microorganisms.
Variational Inverse Control with Events: A General Framework for Data-Driven Reward Definition (2018)

The design of a reward function often poses a major practical challenge to real-world applications of reinforcement learning. Approaches such as inverse reinforcement learning attempt to overcome this challenge, but require expert demonstrations, which can be difficult or expensive to obtain in practice. We propose variational inverse control with events (VICE), which generalizes inverse reinforcement learning methods to cases where full demonstrations are not needed, such as when only samples of desired goal states are available. Our method is grounded in an alternative perspective on control and reinforcement learning, where an agent's goal is to maximize the probability that one or more events will happen at some point in the future, rather than maximizing cumulative rewards. We demonstrate the effectiveness of our methods on continuous control tasks, with a focus on high-dimensional observations like images where rewards are hard or even impossible to specify.
Microbial shift and periodontitis (2010)

Periodontitis, a biofilm-associated inflammatory disease of the periodontium, is a major cause of tooth loss in the world. This disease appears to have multiple etiologies, the most studied of which are microbial and immunological. The primary microbial factor contributing to disease is a shift in the content of the oral microflora, while the primary immunological factor is the destructive host inflammatory response. Several techniques have been used clinically to treat periodontitis, but the most successful ones appear to address both the bacterial and inflammatory components of the condition. Therefore, this review will detail the microbial and molecular nature of periodontitis, and it will also compare the efficacy of traditional and emerging technologies for treating this costly disease.
Elastic Constants of Electron-Beam-Deposited Thin Films of Molybdenum and Aluminum on LiNbO<inf>3</inf> (1983)

The elastic constants and densities of electronbeam-deposited thin films of molybdenum and aluminum on 1289iNb03 have been determined. This was done by comparing UHF SAW device dispersion characteristics, measured entirely while the devices were mounted in a sealed vacuum chamber, with exact computer calculations using isotropic models. A leastsquares fit between the theory and experimental data was used as a basis for the iteration procedure. The departures observed between the measured dispersion curves and dispersion curves calculated from published aggregate constants result mainly from a reduction in the shearstiffnesses of the films.
Optimisation of a two-wire thermal sensor for flow and sound measurements (2002)

The Microflown is an acoustic sensor measuring particle velocity instead of pressure, which is usually measured by conventional microphones. In this paper an analytical model is presented to describe the physical processes that govern the behaviour of the sensor and determine its sensitivity. The Microflown consists of two heaters that act simultaneously as sensors. Forced convection by an acoustic wave leads to a small perturbation of this temperature profile, resulting in a temperature difference between the two sensors. This temperature difference, to which the sensitivity is proportional, is calculated with perturbation theory. Consequently the frequency dependent behaviour of the sensitivity is analysed; it is found that there are two important corner frequencies, the first related to the time constant velocity of heat diffusion between the sensors, the second related to the heat capacity of the heaters. The developed model is verified by experiments. Previously a very good model has been given for the performance of the Microflown in a channel, i.e. with both heaters between fixed walls walls in the positive and negative z-direction. Here, a model is presented that describes the situation of the present used sensors: without walls under and above them. Model predictions are compared to experimental results.
Real-Time Downhole pH Measurement Using Optical Spectroscopy (2007)

Summary A new downhole pH sensor has been developed to provide an in-situ pH measurement of formation water at reservoir conditions, and results are presented for two wells in the Norwegian Sea. The measurement technique, for use with wireline formation-sampling tools, uses pH-sensitive dyes that change color according to the pH of the formation water. To make a real-time pH measurement, the dye is injected into the formation fluid being pumped through the tool flowline, and the relevant visible wavelengths in an optical detector are used to record the dye signal and calculate pH with 0.1-unit accuracy. The pH of a formation fluid alters as the sample is brought to surface from the high-temperature and high-pressure conditions downhole, owing to acid gases and salts coming out of solution and changes in water-chemistry equilibria. To obtain an accurate pH, the measurement must be made downhole at reservoir conditions. Unlike potentiometric methods in which fouling of electrode surfaces by oil and mud is a potential problem, the dye technique is robust because the dye is isolated from the formation fluid and is injected into the sample only when a measurement is made. The technique has been applied successfully to both oil-based and water-based drilling muds, with successful measurements even in mixed oil/water flows. Multiple measurements of pH at a single sampling station demonstrate that the method is robust and repeatable. These measurements have been compared with numerical simulations using a multiphase chemical-equilibrium model that uses laboratory analysis of collected water samples as input. pH is a key parameter in water chemistry and is critical for corrosion and scale studies. Accurate downhole pH measurement allows a more-accurate selection of appropriate completion materials and more-effective planning for scale treatment and inhibition.
Clavicle Trauma: From Acromioclavicular Joint Injuries to Distal Clavicle Fractures and Midshaft Fractures in Contact Athletes. (2019)

Injuries to the clavicle and its articulations (the acromioclavicular and sternoclavicular joints) are becoming increasingly common. Conventional treatment has been dominated by nonsurgical techniques; however, the active patient was often left with substantial residual disability that was underreported. It is now recognized that surgical intervention may be advantageous in specific patients, especially athletes. Surgeons should consider pathophysiology, indications, and surgical techniques to best manage these injuries.
Intragastric balloon for weight loss: results in 100 individuals followed for at least 2.5 years (2009)

Intragastric balloon therapy was relatively innocuous and associated with successful weight loss and maintenance at 2.5 years in a quarter of participants. It represents a valid option for weight loss.
Glycolysis Metabolites and Risk of Atrial Fibrillation and Heart Failure in the PREDIMED Trial (2021)

The increased prevalence of atrial fibrillation (AF) and heart failure (HF) highlights the need to better understand the mechanisms underlying these cardiovascular diseases (CVDs). In the present study, we aimed to evaluate the association between glycolysis-related metabolites and the risk of AF and HF in a Mediterranean population at high risk of CVD. We used two case-control studies nested within the PREDIMED trial. A total of 512 incident AF cases matched to 734 controls, and 334 incident HF cases matched to 508 controls, were included. Plasma metabolites were quantified by using hydrophilic interaction liquid chromatography coupled with high-resolution negative ion mode MS detection. Conditional logistic regression analyses were performed. The results showed no association between baseline plasma glycolysis intermediates and other related metabolites with AF. Only phosphoglycerate was associated with a higher risk of HF (OR <sub>for 1 SD increase</sub>: 1.28; 95% CI: 1.06, 1.53). The present findings do not support a role of the glycolysis pathway in the pathogenesis of AF. However, the increased risk of HF associated with phosphoglycerate requires further studies.
Stretchable Self-Healing Polymeric Dielectrics Cross-Linked Through Metal–Ligand Coordination (2016)

A self-healing dielectric elastomer is achieved by the incorporation of metal-ligand coordination as cross-linking sites in nonpolar polydimethylsiloxane (PDMS) polymers. The ligand is 2,2'-bipyridine-5,5'-dicarboxylic amide, while the metal salts investigated here are Fe(2+) and Zn(2+) with various counteranions. The kinetically labile coordination between Zn(2+) and bipyridine endows the polymer fast self-healing ability at ambient condition. When integrated into organic field-effect transistors (OFETs) as gate dielectrics, transistors with FeCl2 and ZnCl2 salts cross-linked PDMS exhibited increased dielectric constants compared to PDMS and demonstrated hysteresis-free transfer characteristics, owing to the low ion conductivity in PDMS and the strong columbic interaction between metal cations and the small Cl(-) anions which can prevent mobile anions drifting under gate bias. Fully stretchable transistors with FeCl2-PDMS dielectrics were fabricated and exhibited ideal transfer characteristics. The gate leakage current remained low even after 1000 cycles at 100% strain. The mechanical robustness and stable electrical performance proved its suitability for applications in stretchable electronics. On the other hand, transistors with gate dielectrics containing large-sized anions (BF4(-), ClO4(-), CF3SO3(-)) displayed prominent hysteresis due to mobile anions drifting under gate bias voltage. This work provides insights on future design of self-healing stretchable dielectric materials based on metal-ligand cross-linked polymers.
Taking the brakes off telomerase (2015)

Studies using human embryonic stem cells have revealed how common cancer-associated mutations exert their effect on telomerase after cells differentiate into more specialized cell types.
Growth and Development of the California Red Scale, Aonidiella aurantii123 (1968)

Aonidiella aurantii (Maskell) was reared in the laboratory at 25±0.5°C and 70±5% RH. Growth and development between the 2 sexes were correlated. Males passed rapidly through the prepupal, pupal, and adult stages ; comparable 2nd-instar females molted only once more before they became adults. Overall mortality from the crawler stage to adult females was 14.4%, with crawlers being the most susceptible. During August, most males emerged between 5:30 and 6:30 PM (Pacific daylight time) at illumination levels of 350–525 foot-candles, and emergence ceased by 8 PM when illumination levels fell below 1 foot-candle. Almost all males that emerged during a given afternoon were dead the next morning, and males held in continuous light began dying within 2 hours, 50% were dead within 6–7 hours, and all were dead within 14 hours after emergence. In males of identical age, 88% emerged the first 3 days after eclosion, but stragglers continued to emerge for 13 days. Production of crawlers averaged 352 per female with a range of 102–479. Of total crawler production, 55% occurred during the 1st 5 weeks and 90% during the 1st 10 weeks. The longest reproductive period for any female was 25 weeks.
Der Goldene Einband der Theodelinda. Material und form, Ritual und Raum (2011)

Founded in 1683 in Leiden, the Netherlands, Brill is a leading international academic publisher in the Humanities, Social Sciences, International Law, and Biology. With offices in the Netherlands, Germany, Austria, the USA and Asia, Brill today publishes more than 360 journals and 2,000 new books and reference works each year as well as a large number of databases and primary source research collections.
Prosodic Classification of Discourse Markers (2015)

The first contribution of this study is the description of the prosodic behavior of discourse markers present in two speech corpora of European Portuguese (EP) in different domains (university lectures, and map-task dialogues). The second contribution is a multiclass classification to verify, given their prosodic features, which words in both corpora are classified as discourse markers, which are disfluencies, and which correspond to words that are neither markers nor disfluencies (chunks). Our goal is to automatically predict discourse markers and include them in rich transcripts, along with other structural metadata events (e.g., disfluencies and punctuation marks) that are already encompassed in the language models of our in-house speech recognizer. Results show that the automatic classification of discourse markers is better for the lectures corpus (87%) than for the dialogue corpus (84%). Nonetheless, in both corpora, discourse markers are more easily confused with chunks than with disfluencies.
Improving query response time in scientific databases using data aggregation -a case study (2002)

Although most state-of-the-art database systems have no inherent limitations w.r.t. the amount of data they can handle, the huge data quantities typically found in scientific database applications often exceed the feasibility level from a practical point of view when query performance is the issue. One theoretically well-known concept of improving query response time in scientific database applications is using the categorization and classification facilities often found in scientific computing domains for storing data aggregations that allow to substitute expensive access to raw data by the use of stored aggregated values. The results of an empirical performance study carried out in the application domain of market research are presented which substantiate the practical importance of such work. Using real market research data, it is shown that query response time can be shortened in an order of magnitude if a proper data aggregation concept is used. If the data aggregates are designed properly, the overhead of generating and managing materializations of data aggregates is by far outweighed by the improved query performance in realistic scenarios.
Quantum wells, excitons, and lasers at blue-green wavelengths in ZnSe-based heterostructures (1992)

Recent developments were reviewed in ZnSe-based quantum wells and heterostructures with emphasis on physics and engineering towards light emitter applications at blue-green wavelengths. To illustrate current progress, examples are given of both diode laser and light emitting diode device research.
ChemInform Abstract: The Synthesis and Reactivity of a Novel 10‐Membered Azaenediyne. (1997)

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.
Collagenolytic Activity of Some Marine Bacteria (1975)

Reconstituted, acid-extracted collagen was used to prepare a medium to screen proteolytic marine bacteria for their ability to elaborate collagenolytic enzymes. The medium was resistant to solubilization by trypsin, hyaluronidase, chondroitinase ABC, and various marine proteinases, but was readily hydrolyzed by commercial Clostridium collagenases. Eighty-seven marine isolates collected in the vicinity of Bermuda, Oahu (Hawaii), and Stone Harbor and Cape May, N. J., were screened. Approximately 44 per cent of the isolates were capable of elaborating enzymes that hydrolyzed reconstituted collagen gels. Several cultures produced collagenolytic enzymes only when grown in the presence of collagen or degradation products of collagen, and with very few exceptions the presence of collagen in the medium greatly enhanced collagenolytic enzyme production. The enzymes from a collagenolytic Bermuda marine isolate were studied in more detail to illustrate that the enzymes capable of hydrolyzing reconstituted collagen were separable from nonspecific proteinases by zone electrophoresis and that these enzymes were true collagenases by virtue of their ability to hydrolyze native bovine Achilles'tendon obtained from three different sources.
Faculty Opinions recommendation of Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1-CD8+ Tumor-Infiltrating T Cells. (2020)

An improved understanding of the anti-tumor CD8 + T cell response after checkpoint blockade would enable more informed and effective therapeutic strategies. Here we examined the dynamics of the effector response of CD8 + tumor-infiltrating lymphocytes (TILs) after checkpoint blockade therapy. Bulk and single-cell RNA profiles of CD8 + TILs following combined Tim-3+PD-1 blockade in preclinical models revealed significant changes in the transcriptional profile of PD-1 - TILs. These cells could be divided into subsets bearing characterstics of nave-, effector-, and memory-precursor-like cells. Effector-and memory-precursor-like TILs contained tumor-antigen specific cells, exhibited proliferative and effector capacity and expanded in response to different
Turbo coding in ADSL DMT systems (2002)

Increasing the transmission speed and/or the loop length in asymmetric digital subscriber lines (ADSL) is highly desirable. This can be achieved by employing sophisticated channel coding techniques. We investigate the potential usage of turbo codes in ADSL discrete multitone (DMT) systems to improve the system performance. Using turbo coding in ADSL DMT systems is shown to give a 6 dB coding gain at a bit error rate (BER) as low as 10/sup -6/. To lower the decoding complexity, Gray mapping of turbo coded QAM symbols is proposed and a standard binary decoder is employed at the receiver. To counter impulse noise, another major impairment in subscriber loop transmissions, using turbo codes together with proper interleaving and erasure decoding results in very good performance.