gebhart/patrepeval huggingface dataset:
Versatile Product Detection via Coupled Assays for Ultra-high-throughput Screening of Carbohydrate-Active-Enzymes in Microfluidic Droplets (2023)

ABSTRACT Enzyme discovery and directed evolution are the two major contemporary approaches for the improvement of industrial processes by biocatalysis in various fields. Customization of catalysts for improvement of single enzyme reactions or de novo reaction development is often complex and tedious. The success of screening campaigns relies on the fraction of sequence space that can be sampled, whether for evolving a particular enzyme or screening metagenomes. Ultrahigh-throughput screening (uHTS) based on in-vitro compartmentalization in water-in-oil emulsion of picolitre droplets generated in microfluidic systems allows screening rates &gt;1 kHz (or &gt;107 per day). Screening for Carbohydrate Active Enzymes (CAZymes) catalysing biotechnologically valuable reactions in this format presents an additional challenge, because the released carbohydrates are difficult to monitor in high throughput. Activated substrates with large optically active hydrophobic leaving groups provide a generic optical readout, but the molecular recognition properties of sugars will be altered by incorporation of such fluoro- or chromophores and their typically higher reactivity, as leaving groups with lowered pKa values compared to native substrates make observation of promiscuous reactions more likely. To overcome these issues, we designed microdroplet assays in which optically inactive carbohydrate products are made visible by specific cascades: the primary reaction of an unlabelled substrate leads to an optical signal downstream. Successfully implementing such assays at the picoliter droplet scale allowed us to detect glucose, xylose, glucuronic acid and arabinose as final products of complex oligosaccharide degradation by glycoside hydrolases by absorbance measurements. Enabling the use of uHTS for screening CAZyme reactions that have been thus far elusive will chart a route towards faster and easier development of specific and efficient biocatalysts for biovalorisation, directing enzyme discovery towards catalysts for their natural rather than model substrates. Graphical abstract / TOC
Biochemical Aspects of Syneresis: A Review (1989)

Syneresis is the process in cheese manufacture whereby the whey component of milk is expelled following curd formation. Factors that interfere with syneresis affect the moisture content and quality of the final producL This article reviews the various reported methods for experimentally measuring syneresis and the effect on syneresis of variables including pH, temperature, salt concentration, milk composition and concentration, and effects of milk pretreaunent. A recently developed method for the measurement of syneresis on a small scale has allowed the effect of varying casein composition to be studied. Syneresis is sensitive to the concentration of ~-casein and also to low levels of dephosphorylation of ~casein. IS-Casein, therefore, seems to play an important role in syneresis and may affect micelle surface properties. Syneresis depends at the protein level on a combination of specific and nonspecific interactions, many of which also occur during curd formation.
Promotion of mouse ameloblast proliferation by Lgr5 mediated integrin signaling (2013)

Rodent incisors grow throughout the animal's lives, and the tooth-forming cells are provided from proximal ends of the incisors where the tooth epithelium forms a stem cell niche called cervical loop. The committing cells in a cervical loop actively begin to proliferate (pre-ameloblasts), and differentiating into ameloblasts. This study showed that the lower incisors of mice null for CD61 (CD61(-/-) ), also known as integrin β3, were significantly shorter than those of the wild-type mice at 8-week-old. The protein and mRNA expressions levels of Fgfr2, Lgr5, and Notch1, which are known to be involved in pre-ameloblastic cell proliferation and stem cell maintenance, were reduced in the cervical loop of 2-week-old CD61(-/-) mice. The proliferation of pre-ameloblasts was reduced in CD61(-/-) ameloblasts. The siRNA-mediated suppression of CD61 (siCD61) reduced the proliferation of pre-ameloblastic cell line ALC, and the expression levels of Lgr5 and Notch1 were reduced by the transfection with siCD61. The suppression of Lgr5 by transfection with siLgr5 suppressed the proliferation of the ALC cells. These results suggested that CD61 signaling is required for the proper growth of the cervical loop and for the promotion of the proliferation of pre-ameloblastic cells through Lgr5.
$A^{4}NT$: Author Attribute Anonymity by Adversarial Training of Neural\n Machine Translation (2017)

Text-based analysis methods allow to reveal privacy relevant author\nattributes such as gender, age and identify of the text's author. Such methods\ncan compromise the privacy of an anonymous author even when the author tries to\nremove privacy sensitive content. In this paper, we propose an automatic\nmethod, called Adversarial Author Attribute Anonymity Neural Translation\n($A^4NT$), to combat such text-based adversaries. We combine\nsequence-to-sequence language models used in machine translation and generative\nadversarial networks to obfuscate author attributes. Unlike machine translation\ntechniques which need paired data, our method can be trained on unpaired\ncorpora of text containing different authors. Importantly, we propose and\nevaluate techniques to impose constraints on our $A^4NT$ to preserve the\nsemantics of the input text. $A^4NT$ learns to make minimal changes to the\ninput text to successfully fool author attribute classifiers, while aiming to\nmaintain the meaning of the input. We show through experiments on two different\ndatasets and three settings that our proposed method is effective in fooling\nthe author attribute classifiers and thereby improving the anonymity of\nauthors.\n
Social Choice Random Utility Models of Intransitive Pairwise Comparisons (2018)

There is a growing need for discrete choice models that account for the complex nature of human choices, escaping traditional behavioral assumptions such as the transitivity of pairwise preferences. Recently, several parametric models of intransitive comparisons have been proposed, but in all cases the maximum likelihood problem is non-concave, making inference difficult. In this work we generalize this trend, showing that there cannot exist any parametric model with a concave log-likelihood function that can exhibit intransitive preferences. Given this result, we motivate a new model for analyzing intransitivity in pairwise comparisons, taking inspiration from the Condorcet method (majority vote) in social choice theory. The Majority Vote model we analyze is defined as a voting process over independent Random Utility Models (RUMs). We infer a multidimensional embedding of each object or player, in contrast to the traditional one-dimensional embedding used by models such as the Thurstone or Bradley-Terry-Luce (BTL) models. We show that a three-dimensional majority vote model is capable of modeling arbitrarily strong and long intransitive cycles, and can also represent arbitrary pairwise comparison probabilities on any triplet. We provide experimental results that substantiate our claims regarding the effectiveness of our model in capturing intransitivity for various pairwise choice tasks such as predicting choices in recommendation systems, winners in online video games, and elections.
Scaling (2013)

Abstract Scaling is one of the most vexing problems affecting the use of membranes for pressure‐driven desalination. The scaling problems most commonly encountered are caused by calcium carbonate, calcium sulfate, and silica in brackish water RO; calcium carbonate and calcium sulfate in seawater RO; and calcium carbonate and calcium phosphate in desalination of municipal wastewater. This article surveys the conditions leading to scaling, mechanisms by which scaling can cause flux decline, thermodynamics and kinetics of scaling, present state of the art in preventing scaling, new processes proposed for mitigating the problem, and new techniques for detecting the onset of scaling.
Assessment of cement introduction and pressurisation techniques used in total hip arthroplasty (2004)

Recent studies, including the Swedish Hip Register, have confirmed that modern cementing techniques are important to achieve long-term implant survival. Their ultimate goal is to obtain an increased strength of cement and its interfaces with bone, thereby maintaining secure fixation and effective load transmission. The objective of this study was to measure the medullary pressures generated during bone cement injection, pressurisation and femoral prosthesis insertion for total hip arthroplasty. The measurements were recorded throughout the length of an in vitro femoral model while implanting a series of prosthetic hip stems using different pressurisation techniques. The prostheses used were the Charnley 40 flanged stem, an Exeter No. 3 stem, and a custom primary femoral component used in Belfast (Johnson & Johnson, DePuy International Ltd.). The following parameters were derived from the pressure data recorded; peak pressure, decay pressure and duration above 76 kPa, the pressure regarded as the threshold to obtain adequate bone penetration. The range of peak distal stem pressures expected for all stems was 200–500kPa. The custom and Exeter stems generated proximal cement pressures in the range 100–300kPa. These pressures were attained through cement containment by stem design or auxiliary pressurising devices, respectively. It was observed that the Charnley femoral component did not perform as well with regard to proximal pressurisation, irrespective of which pressurisation technique was implemented. The durations of pressure maintenance above 76kPa are also important, 5 seconds being accepted as a minimum for an effective interface. These results reflect the pressure measurements, with adequate durations being maintained by those stems and pressurisers that were characterised by higher peak pressures. It is concluded that stem design and the complementary cement management techniques are essential to realise the pressure/time characteristics that are regarded as necessary to form an optimum bone/cement interface.
Design and implementation of an SF/sub 6/ interrupting chamber applied to low range generator circuit breakers suitable for interruption of current having a non-zero passage (2002)

New types of SF/sub 6/ interrupting chambers, which implement innovative interrupting principles, have been developed during the past years, based on the objectives of reducing the operating energy of the circuit breakers and consequently increasing their reliability. This paper describes the rear-exhaust-type "self blast" double-volume thermal chamber, which was designed with the help of new chamber development software programs, of the physical imaging model of the arc. Simulations and confirmation by laboratories tests the interruption of short-circuit currents and, especially, the testing of short-circuit currents that have a nonpassage by zero on such a new chamber for applications to generator circuit breakers are shown and evaluated.
Biosynthesis of the Myxobacterial Antibiotic Corallopyronin A (2010)

Corallopyronin A is a myxobacterial compound with potent antibacterial activity. Feeding experiments with labelled precursors resulted in the deduction of all biosynthetic building blocks for corallopyronin A and revealed an unusual feature of this metabolite: its biosynthesis from two chains, one solely PKS-derived and the other NRPS/PKS-derived. The starter molecule is believed to be carbonic acid or its monomethyl ester. The putative corallopyronin A biosynthetic gene cluster is a trans-AT-type mixed PKS/NRPS gene cluster, containing a beta-branching cassette. Striking features of this gene cluster are a NRPS-like adenylation domain that is part of a PKS-type module and is believed to be responsible for glycine incorporation, as well as split modules with individual domains occurring on different genes. It is suggested that CorB is a trans-acting ketosynthase and it is proposed that it catalyses the Claisen condensation responsible for the interconnection of the two chains. Additionally, the stereochemistry of corallopyronin A was deduced by a combination of a modified Mosher's method and ozonolysis with subsequent chiral GC analyses.
Successful <i>in Vitro</i> Fertilization with Sperm Cells from a Man with Immune Infertility (1985)

In vitro fertilization and embryo transfer was carried out in a couple that has been infertile for 7 years. High titers of antisperm autoantibodies in the husband's serum are (table, see text) believed to be the main cause of their infertility. Prolonged methylprednisolone treatment of the man combined with artificial insemination remained unsuccessful. In two IVF attempts embryos were obtained and replaced using capacitated sperm of the husband. A pregnancy was established in the second IVF cycle, but a spontaneous abortion followed after 6 weeks of amenorrhea.
Synthesis of Hyperbranched Carbohydrate Polymers by Ring‐Opening Multibranching Polymerization of Anhydro Sugar (2007)

The synthesis of novel hyperbranched carbohydrate polymers, prepared by the ring-opening multibranching polymerizations of anhydro and dianhydro sugars, is described. The hyperbranched carbohydrate polymers were formed by the cationic polymerization of 1,6-anhydro-beta-D-hexopyranose, 1,4-anhydrotetritol, 2,3-anhydrotetritol, and 1,2:5,6-dianhydro-D-mannitol. These polymerizations proceeded without gelation to produce water-soluble hyperbranched carbohydrate polymers with controlled molecular weights and narrow polydispersities. The values for the degree of branching of the polymers were in the range of 0.28-0.50. The polymerization method, which proceeds through a ring-opening reaction by a proton-transfer reaction mechanism, is a facile method leading to a spherical carbohydrate polymer with a high degree of branching.
Effects of reflow conditions on the formation of Au-Ni-Sn compounds at the interface of Au-Pb-Sn and Au-Sn solder joints with Ni substrate (2003)

We investigated the effect of reflow conditions (temperature and time above the liquidus temperature) on the growth, morphology and location of the ternary (Au,Ni)Sn/sub 4/ phase in joints made with Ni or Au/Ni substrates. We considered joints created with Au/sub 0.1/Sn/sub 99.9/ or Au/sub 0.1/Pb/sub 26/Sn/sub 73.9/ solders reflowed on Ni substrates, and Sn/sub 94.35/Ag/sub 3.8/Cu/sub 1.85/ solder reflowed on Au/Ni metallization. The Au/sub 0.1/Pb/sub 26/Sn/sub 73.9/ solder alloy reflowed on a Ni substrate at 185/spl deg/C for 30 s above liquidus and subsequently annealed at 150/spl deg/C gave rise to two layers of intermetallic compounds at the solder/substrate interface, Ni/sub 3/Sn/sub 4/ and (Au, Ni)Sn/sub 4/. However, when this solder alloy was reflowed at 235/spl deg/C for 30 s above liquidus, only one interface layer was observed, Ni/sub 3/Sn/sub 4/, while the (Au,Ni)Sn/sub 4/ ternary phase was found to grow in the bulk of the solder. The SnAgCu/Au/Ni joints were reflowed for 74 s above liquidus and the peak temperature attained was 244/spl deg/C. (Au,Ni)Sn/sub 4/ phase was observed to form in the bulk of these joints upon reflow, with a Cu content less than 1 atomic percent. This intermetallic compound remained in the bulk of the joint as the samples were annealed at 150/spl deg/C up to 261 hours. For the Au/sub 0.1/Sn/sub 99.9//Ni system, only one layer, the Ni/sub 3/Sn/sub 4/ phase, was found to grow at the solder/substrate interface, both after reflow (at 260/spl deg/C for 46 s above liquidus) and for an annealing schedule at 150/spl deg/C of up to 49 hours.
A Mass Spectrometry-Based Profiling of Interactomes of Viral DDB1- and Cullin Ubiquitin Ligase-Binding Proteins Reveals NF-κB Inhibitory Activity of the HIV-2-Encoded Vpx (2018)

Viruses and hosts are situated in a molecular arms race. To avoid morbidity and mortality, hosts evolved antiviral restriction factors. These restriction factors exert selection pressure on the viruses and drive viral evolution toward increasingly efficient immune antagonists. Numerous viruses exploit cellular DNA damage-binding protein 1 (DDB1)-containing Cullin RocA ubiquitin ligases (CRLs) to induce the ubiquitination and subsequent proteasomal degradation of antiviral factors expressed by their hosts. To establish a comprehensive understanding of the underlying protein interaction networks, we performed immuno-affinity precipitations for a panel of DDB1-interacting proteins derived from viruses such as mouse cytomegalovirus (MCMV, Murid herpesvirus [MuHV] 1), rat cytomegalovirus Maastricht MuHV2, rat cytomegalovirus English MuHV8, human cytomegalovirus (HCMV), hepatitis B virus (HBV), and human immunodeficiency virus (HIV). Cellular interaction partners were identified and quantified by mass spectrometry (MS) and validated by classical biochemistry. The comparative approach enabled us to separate unspecific interactions from specific binding partners and revealed remarkable differences in the strength of interaction with DDB1. Our analysis confirmed several previously described interactions like the interaction of the MCMV-encoded interferon antagonist pM27 with STAT2. We extended known interactions to paralogous proteins like the interaction of the HBV-encoded HBx with different Spindlin proteins and documented interactions for the first time, which explain functional data like the interaction of the HIV-2-encoded Vpr with Bax. Additionally, several novel interactions were identified, such as the association of the HIV-2-encoded Vpx with the transcription factor RelA (also called p65). For the latter interaction, we documented a functional relevance in antagonizing NF-κB-driven gene expression. The mutation of the DDB1 binding interface of Vpx significantly impaired NF-κB inhibition, indicating that Vpx counteracts NF-κB signaling by a DDB1- and CRL-dependent mechanism. In summary, our findings improve the understanding of how viral pathogens hijack cellular DDB1 and CRLs to ensure efficient replication despite the expression of host restriction factors.
Qualitative Real-Time Schlieren and Shadowgraph Imaging of Human Exhaled Airflows: An Aid to Aerosol Infection Control (2011)

Using a newly constructed airflow imaging system, airflow patterns were visualized that were associated with common, everyday respiratory activities (e.g. breathing, talking, laughing, whistling). The effectiveness of various interventions (e.g. putting hands and tissues across the mouth and nose) to reduce the potential transmission of airborne infection, whilst coughing and sneezing, were also investigated. From the digital video footage recorded, it was seen that both coughing and sneezing are relatively poorly contained by commonly used configurations of single-handed shielding maneuvers. Only some but not all of the forward momentum of the cough and sneeze puffs are curtailed with various hand techniques, and the remaining momentum is disseminated in a large puff in the immediate vicinity of the cougher, which may still act as a nearby source of infection. The use of a tissue (in this case, 4-ply, opened and ready in the hand) proved to be surprisingly effective, though the effectiveness of this depends on the tissue remaining intact and not ripping apart. Interestingly, the use of a novel 'coughcatcher' device appears to be relatively effective in containing coughs and sneezes. One aspect that became evident during the experimental procedures was that the effectiveness of all of these barrier interventions is very much dependent on the speed with which the user can put them into position to cover the mouth and nose effectively.From these qualitative schlieren and shadowgraph imaging experiments, it is clear that making some effort to contain one's cough or sneeze puffs is worthwhile. Obviously, there will be a large amount of variation between individuals in the exact hand or tissue (the most common methods) configuration used for this and other practical factors may hinder such maneuvers in daily life, for example, when carrying shopping bags or managing young children.
Adaptive model-based control of boundary impedance in an acoustic impedance tube (2020)

Impedance tubes are employed for measurements of acoustic properties in various fluids. The ability to manipulate and control the frequency-dependent boundary impedance of the tube improves the accuracy of the estimation. Passive solutions, which use composite materials to change the boundary impedance, have been used in the past, and these enable one to realize a finite combination of boundary impedances. In this paper, the tube boundary impedance is being tuned at will by using two loudspeakers, one at each tube’s end. The suggested method operates in the presence of dispersion by estimating, in real-time, a parametric reduced-order model using a multichannel least mean square algorithm. The identified model is fed to a nonlinear, adaptive control algorithm to realize modal traveling wave ratio control. It has been noted that the traveling wave ratio is smooth and parabolic with respect to a second actuator’s complex amplitude across closed regions in the parameter space, thus assuring the convergence of the nonlinear control. An experimental case study utilizing an air-filled impedance tube with two loudspeakers is presented. The results demonstrate the ability to control the dynamics of the principal acoustic mode at will. Thus, enabling one to set the desired tube’s boundary impedance.
ERCC1 as predictive biomarker to platinum-based chemotherapy in adrenocortical carcinomas (2017)

ERCC1 expression is not directly associated with sensitivity to PBC in ACC. Thus, other predictive biomarkers are required to support treatment decisions in patients with ACC.
Design of a high-density SoC FPGA at 20nm (2014)

This article consists of a collection of slides from the author's conference presentation on the special features, system design and architectures, processing capabilities, and targeted markets for Altera's Arria 10 family of processor products.
Quantitative Electron Microscopic Investigation of the Pore Structure in 10:90 Colloidal Silica/Potassium Silicate Sol‐Gels (1990)

Transmission electron microscopy (TEM), scanning electron microscopy (SEM), mercury intrusion porosimetry (MIP), and nitrogen sorption technique (BET) were utilized to characterize the microstructure of a 10:90 wt% colloidal silica/potassium silicate gel as first described by Shoup. Gels in the unsintered state (15% theoretical density) were prepared for microscopy by the techniques of ultramicrotomy, Pt/C replication, and pore casting. Electron microscopic images of the ultramicrotomed thin sections (70 nm) show that the unfired gel possesses three distinct species of pores which are referred to as the micropores, mesopores, and macropores. The average micropore diameter was found to be 4 nm as determined by nitrogen desorption. Quantitative stereological analysis of the ultramicrotomed sections indicated that the average circular and lengthwise dimensions of the cylindrical mesopores were 0.15 and 0.39 μm, respectively. Similarly, this same analysis determined the average spherical macropore diameter to be 0.83 μm. In contrast, MIP results suggested that these gels possessed a unimodal pore size distribution centered around the 0.2‐μm pore size. The discrepancy between MIP and microscopy can be explained by viewing the void space as a pore‐throat network. Experimental evidence for this type of pore geometry was obtained from stereo pairs of Pt/C replicas and thick microtomed sections (0.5 μm) which gave information about particle connectivity and pore casts which depicted the pore connectivity in three dimensions.