gebhart/patrepeval huggingface dataset:
Methods for Improving Enzymatic Trans-glycosylation for Synthesis of Human Milk Oligosaccharide Biomimetics (2014)

Recently, significant progress has been made within enzymatic synthesis of biomimetic, functional glycans, including, for example, human milk oligosaccharides. These compounds are mainly composed of N-acetylglucosamine, fucose, sialic acid, galactose, and glucose, and their controlled enzymatic synthesis is a novel field of research in advanced food ingredient chemistry, involving the use of rare enzymes, which have until now mainly been studied for their biochemical significance, not for targeted biosynthesis applications. For the enzymatic synthesis of biofunctional glycans reaction parameter optimization to promote "reverse" catalysis with glycosidases is currently preferred over the use of glycosyl transferases. Numerous methods exist for minimizing the undesirable glycosidase-catalyzed hydrolysis and for improving the trans-glycosylation yields. This review provides an overview of the approaches and data available concerning optimization of enzymatic trans-glycosylation for novel synthesis of complex bioactive carbohydrates using sialidases, α-l-fucosidases, and β-galactosidases as examples. The use of an adequately high acceptor/donor ratio, reaction time control, continuous product removal, enzyme recycling, and/or the use of cosolvents may significantly improve trans-glycosylation and biocatalytic productivity of the enzymatic reactions. Protein engineering is also a promising technique for obtaining high trans-glycosylation yields, and proof-of-concept for reversing sialidase activity to trans-sialidase action has been established. However, the protein engineering route currently requires significant research efforts in each case because the structure-function relationship of the enzymes is presently poorly understood.
Arthroscopic Laminar Spreader for Rotator Cuff Repair (2022)

Arthroscopic rotator cuff repair can be challenging and requires adequate visualization and space. However, the narrow subacromial space can make difficult to perform tendon release and repair under arthroscopy. Inadequate visualization may lead to inaccurate suture placement, compromising the reduction and fixation of the repaired rotator cuff tendons. Manual or mechanical distraction (using an arm positioner) can be used to increase the working space. However, consistent distraction is very difficult to maintain manually over time due to fatigue, whereas mechanical distraction may overstretch the brachial plexus. To overcome these difficulties, we describe a technique using a specific laminar spreader for subacromial distraction during arthroscopic rotator cuff repair. The arthroscopic laminar spreader, inserted into the subacromial space, is used to distract the humeral head inferiorly from the acromion, improving subacromial space visualization and enabling easily rotator cuff release and repair. The shoulder distraction device improves the surgeon's performance without surgical assistance and allows reducing the operative time with safety. It can be also used anteriorly (to repair the subscapularis) or posteriorly (to repair the infraspinatus and teres minor) or to perform other procedures like superior capsular reconstruction or additional patch.
Growth of GaN films on GaAs substrates in an As-free environment (2006)

We investigated growth of GaN films on [001] GaAs substrates by plasma-assisted molecular beam epitaxy in an As-free chamber. The crystalline quality and the surface morphology of the films were studied with x-ray diffraction and transmission electron, scanning electron, and atomic force microscopes. We determined that direct GaN deposition on the thermally desorbed substrate resulted in the growth of a polycrystalline film containing misoriented grains and inclusions. We achieved a significant improvement of the film quality by adopting a procedure consisting of a substrate nitridation, deposition of a low-temperature buffer layer, and a high-temperature overgrowth.
Parcellation‐based tractographic modeling of the dorsal attention network (2019)

We present a tractographic model of the DAN. This model comprises parcellations within the frontal, parietal, and occipital cortices principally linked through the superior longitudinal fasciculus. Future studies may refine this model with the ultimate goal of clinical application.
Al-2.5 Aerial Image (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Elongation of Fe-Fe atomic pairs in the Invar alloy Fe65Ni35 (2021)

In this study, atomic-scale origin of the Invar effect, which is nearly-zero thermal expansion observed in the Invar alloy ${\mathrm{Fe}}_{65}{\mathrm{Ni}}_{35}$, was investigated by reverse Monte Carlo analysis using complementary data sets of extended x-ray absorption fine structure and x-ray diffraction. The interatomic distances of the nearest neighboring Fe-Fe atomic pairs were $\ensuremath{\sim}0.02$ \AA{} longer than those of the Fe-Ni and Ni-Ni pairs at the minimum pressure in this study (0.6 GPa). The elongation in the Fe-Fe pairs was suppressed with increasing pressure, and the distances of the three pairs were comparable under pressures above the magnetic transition from ferromagnetic to paramagnetic phase at ${P}_{\text{c}}\ensuremath{\approx}7$ GPa. Therefore, the Fe-Fe pairs dominantly contribute to the volume expansion due to the magnetovolume effect. Because a similar magnitude of elongation was observed in the Fe-Fe pairs of a non-Invar Fe-Ni alloy, we conclude that the Invar effect originates from the delicate balance between the number of Fe-Fe pairs and their elongation depending on the magnetization.
Elastic and Mechanical Properties of the MAX Phases (2011)

The more than 60 ternary carbides and nitrides, with the general formula M n +1 AX n —where n = 1, 2, or 3; M is an early transition metal; A is an A-group element (a subset of groups 13–16); and X is C and/or N—represent a new class of layered solids, where M n +1 X n layers are interleaved with pure A-group element layers. The growing interest in the M n +1 AX n phases lies in their unusual, and sometimes unique, set of properties that can be traced back to their layered nature and the fact that basal dislocations multiply and are mobile at room temperature. Because of their chemical and structural similarities, the MAX phases and their corresponding MX phases share many physical and chemical properties. In this paper we review our current understanding of the elastic and mechanical properties of bulk MAX phases where they differ significantly from their MX counterparts. Elastically the MAX phases are in general quite stiff and elastically isotropic. The MAX phases are relatively soft (2–8 GPa), are most readily machinable, and are damage tolerant. Some of them are also lightweight and resistant to thermal shock, oxidation, fatigue, and creep. In addition, they behave as nonlinear elastic solids, dissipating 25% of the mechanical energy during compressive cycling loading of up to 1 GPa at room temperature. At higher temperatures, they undergo a brittle-to-plastic transition, and their mechanical behavior is a strong function of deformation rate.
Cycloheximide speeds the porcine oocyte nuclear kinetics and retains embryonic developmental potential in the presence of gonadotrophins (2010)

Animal embryo engineering requires large amounts of synchronized mature oocytes in vitro. However, porcine cumulus-oocyte complexes aspirated from 3-8 mm follicles are at different germinal vesicle stages. They reach metaphase II stages asynchronously when cultured in vitro. In this study, we examined the effects of pretreatment with or without cycloheximide (CHX), equine chorionic gonadotrophin (eCG), human chorionic gonadotrophin (hCG), and their combinations on meiotic synchronization and the developmental competence of porcine oocytes in vitro following electrical activation. The COCs were pretreated for 12 h with either control medium (TCM 199), CHX (TCM 199 + CHX), eCG/hCG (TCM 199 + eCG/hCG) or eCG/hCG + CHX (TCM 199 + CHX + eCG/hCG), and then cultured for up to 32 h with TCM199 + eCG/hCG. After 12 h pretreatment, the rates of germinal vesicle breakdown (GVBD) were lower (P &lt; 0.05) in the CHX (8.4%) and eCG/hCG + CHX (1.5%) groups compared with control (55.4%) and eCG/hCG (27.2%) groups. After removal of CHX and culture for an additional 12 h in vitro, the majority of the oocytes were synchronized at the GVBD stage in CHX (75.6%) and eCG/hCG + CHX (65.0%) groups. At additional 32 h of culture, the rate of oocytes in metaphase II in eCG/hCG + CHX group (68.3%) was significantly (P &lt; 0.05) higher than the eCG/hCG group (54.8%), but did not differ from other groups (control: 61.3%, CHX: 58.8%). After electrical activation, the cleavage and blastocyst formation rates in the CHX group (80.3%; 19.5%) were significantly (P &lt; 0.05) lower than those in the control group (95.5%; 45.3%), while no difference was found between eCG/hCG + CHX (82.2%; 34.4%) and control groups. Our data, hence, demonstrate pretreatment with CHX hastened nuclear kinetics of porcine oocytes cultured in vitro; however, embryo development potential was retained only when gonadotrophins is present in the in vitro maturation (IVM) medium. Thus, CHX should be used in the two-step culture systems in combination with gonadotrophins. Key words: Oocyte meiosis, synchronization, cycloheximide, embryo development, pig
Distributed cognitive spectrum sensing via group sparse total least-squares (2011)

Dynamic re-use of licensed bands under the hierarchical spectrum access paradigm calls for innovative network-level sensing algorithms for spectrum opportunity awareness in the frequency, time, and space dimensions. Toward this direction, the present paper develops a distributed spectrum sensing algorithm whereby cognitive radios (CRs) cooperate to localize active primary user (PU) transmitters, and estimate their transmit-power spectral densities. The sensing scheme relies on a parsimonious linear system model that accounts for two forms of sparsity: one due to the narrow-band nature of PU transmissions compared to the large swath of monitored frequencies; and another one emerging when employing a spatial grid of candidate PU locations. Capitalizing on this dual sparsity, and combining the merits of Lasso, group Lasso, and total least-squares (TLS), a group sparse (GS) TLS problem is formulated to obtain hierarchically-sparse model estimates, and cope with model uncertainty induced by channel randomness, and grid-induced model offsets. The GS-TLS problem is collaboratively solved by the CRs in a distributed fashion, using only local message exchanges among neighboring nodes. In spite of the non-convexity of the GS-TLS criterion, the novel distributed algorithm has guaranteed convergence to (at least) a locally optimal solution. The analytical findings are corroborated by numerical tests.
‐mapping with the transient phase of unbalanced steady‐state free precession (2013)

Simulations, phantom, and in vivo measurements showed that B1-TRAP offers a good compromise with respect to speed, robustness, and accuracy.
Auxin and cytokinin relationships in 24 microalgal strains1 (2013)

Endogenous auxins and cytokinins were quantitated in 24 axenic microalgal strains from the Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Charophyceae. These strains were in an exponential growth phase, being harvested on day 4. Acutodesmus acuminatus Mosonmagyaróvár Algal Culture Collection-41 (MACC) produced the highest biomass and Chlorococcum ellipsoideum MACC-712 the lowest biomass. The auxins, indole-3-acetic acid (IAA) and indole-3-acetamide (IAM) were present in all microalgal strains. No other auxin conjugates were detected. IAA and IAM concentrations varied greatly, ranging from 0.50 to 71.49 nmol IAA · g(-1) DW and 0.18 to 99.83 nmol IAM · g(-1) DW, respectively. In 19 strains, IAA occurred in higher concentrations than IAM. Nineteen cytokinins were identified in the microalgal strains. Total cytokinin concentrations varied, ranging from 0.29 nmol · g(-1) DW in Klebsormidium flaccidum MACC-692 to 21.40 nmol · g(-1) DW in Stigeoclonium nanum MACC-790. The general trend was that cis-zeatin types were the predominant cytokinins; isopentenyladenine-type cytokinins were present in moderate concentrations, while low levels of trans-zeatin-type and very low levels of dihydrozeatin-type cytokinins were detected. Ribotides were generally the main cytokinin conjugate forms present with the cytokinin free bases and ribosides present in similar but moderate levels. The levels of O-glucosides were low. Only one N-glucoside was detected, being present in nine strains in very low concentrations. In 15 strains, the auxin content was 2- to 4-fold higher than the cytokinin content.
A High-Frequency Link Three-Phase Dual-Inverter System Using Two Phase-Shifted Single-Phase Series Resonant Inverters. (1992)

A novel inverter system to synthesize three-phase sinusoidal currents with a combination of two units using two phase-shifted single-phase series resonant inverters is proposed. The structure and
Interactive clustering for navigating in hypermedia systems (1994)

This paper talks about clustering related nodes of an overview diagram to reduce its complexity and size. This is because although overview diagrams are useful for helping the user to navigate in a hypermedia system, for any real-world system these become too complicated and large to be really useful. Both structure-based and content-based clustering are used. Since the nodes can be related to each other in different ways, depending on the situation different clustered views will be useful. Hence, it should be possible to interactively specify the clustering conditions and examine the resulting views. We present efficient clustering algorithms which can cluster the information space in real-time. We talk about the Navigational View Builder, a tool that allows the interactive development of overview diagrams. Finally, we propose a 3-dimensional approach for visualizing these abstracted views.
Evaluation of osteopenia and osteoporosis in younger breast cancer survivors compared with cancer-free women: a prospective cohort study (2018)

Younger breast cancer survivors are at higher risk for osteopenia and osteoporosis compared to cancer-free women. Studies are needed to determine effective approaches to minimize bone loss in this population.
Online collaborative approach to teaching hands-on photonic integrated circuit (PIC) device testing (Conference Presentation) (2022)

PIC device concepts are difficult to grasp, and explanations typically require the solution of Maxwell’s equations. Laboratory experiments which demonstrate the testing of these devices can offer some intuition into device functionality. However, photonics device test on an unpackaged die requires a complicated equipment set-up because devices, both passive (all optical) and active (opto-electronic), need precise (~nm) optical alignment. Online asynchronous courses, Integrated Photonics Test: Passive Devices (IPT:Passive) and Integrated Photonics Test: Active Devices (IPT:Active), that teach hands-on laboratory testing of volume-manufactured photonic integrated circuit (PIC) devices are created as a multi-instructor collaborative approach with lectures and laboratory videos and exercises.
Ca2+Binding and Conformational Changes in a Calmodulin Domain (1998)

Calcium activation of the C-terminal domain of calmodulin was studied using 1H and 15N NMR spectroscopy. The important role played by the conserved bidentate glutamate Ca2+ ligand in the binding loops is emphasized by the striking effects resulting from a mutation of this glutamic acid to a glutamine, i.e. E104Q in loop III and E140Q in loop IV. The study involves determination of Ca2+ binding constants, assignments, and structural characterizations of the apo, (Ca2+)1, and (Ca2+)2 states of the E104Q mutant and comparisons to the wild-type protein and the E140Q mutant [Evenäs et al. (1997) Biochemistry 36, 3448-3457]. NMR titration data show sequential Ca2+ binding in the E104Q mutant. The first Ca2+ binds to loop IV and the second to loop III, which is the order reverse to that observed for the E140Q mutant. In both mutants, the major structural changes occur upon Ca2+ binding to loop IV, which implies a different response to Ca2+ binding in the N- and C-terminal EF-hands. Spectral characteristics show that the (Ca2+)1 and (Ca2+)2 states of the E104Q mutant undergo global exchange on a 10-100 micros time scale between conformations seemingly similar to the closed and open structures of this domain in wild-type calmodulin, paralleling earlier observations for the (Ca2+)2 state of the E140Q mutant, indicating that both glutamic acid residues, E104 and E140, are required for stabilization of the open conformation in the (Ca2+)2 state. To verify that the NOE constraints cannot be fulfilled in a single structure, solution structures of the (Ca2+)2 state of the E104Q mutant are calculated. Within the ensemble of structures the precision is good. However, the clearly dynamic nature of the state, a large number of violated distance restraints, ill-defined secondary structural elements, and comparisons to the structures of calmodulin indicate that the ensemble does not provide a good picture of the (Ca2+)2 state of the E104Q mutant but rather represents the distance-averaged structure of at least two distinct different conformations.
A 256 x 256 compact cmos image sensor with on-chip motion detection function (2003)

A 256×256 CMOS passive pixel image sensor with especially equipped simple switches, which enables motion detection, is implemented. Each pixel consists of a simple combination of a photodiode and an address switch. Photocharge generated at each pixel is converted to voltage by means of a column charge amplifier array, and motion detection has been realized with utilizing the photodiode as a frame memory. Its output is transformed to a digital value with a 128 array 8-bit analog-to-digital (A/D) converter. Simultaneously, fixed pattern noise is suppressed by utilizing A/D conversion as the CDS circuit. Due to its simple structure, more than 70% fill factor ratio has been realized. The extracted motion detection results can be displayed digitally at 128 frames per second by means of 128 A/D converter arrays.
A Process for Etching Modulated Profiles (2008)

A process for spot repair of damaged anodized aluminum panels is described. The process is based on etching the aluminum oxide layer using special fixtures that provide controlled, gradual transitions of the etched profile, enabling the fabrication of "borderline"-free repaired regions. The process does not require the application of etching masks. The profile of the etched region is solely controlled by the geometry of the specially developed etching fixture. Excellent agreement has been noted between experimental results and transport controlled models that predict the etching profile.
In-situ biogas upgrading during anaerobic digestion of food waste amended with walnut shell biochar at bench scale (2017)

A modified version of an in-situ CO<sub>2</sub> removal process was applied during anaerobic digestion of food waste with two types of walnut shell biochar at bench scale under batch operating mode. Compared with the coarse walnut shell biochar, the fine walnut shell biochar has a higher ash content (43 vs. 36 wt%) and higher concentrations of calcium (31 vs. 19 wt% of ash), magnesium (8.4 vs. 5.6 wt% of ash) and sodium (23.4 vs. 0.3 wt% of ash), but a lower potassium concentration (0.2 vs. 40% wt% of ash). The 0.96-3.83 g biochar (g VS<sub>added</sub>)<sup>-1</sup> fine walnut shell biochar amended digesters produced biogas with 77.5%-98.1% CH<sub>4</sub> content by removing 40%-96% of the CO<sub>2</sub> compared with the control digesters at mesophilic and thermophilic temperature conditions. In a direct comparison at 1.83 g biochar (g VS<sub>added</sub>)<sup>-1</sup>, the fine walnut shell biochar amended digesters (85.7% CH<sub>4</sub> content and 61% CO<sub>2</sub> removal) outperformed the coarse walnut shell biochar amended digesters (78.9% CH<sub>4</sub> content and 51% CO<sub>2</sub> removal). Biochar addition also increased alkalinity as CaCO<sub>3</sub> from 2800 mg L<sup>-1</sup> in the control digesters to 4800-6800 mg L<sup>-1</sup>, providing process stability for food waste anaerobic digestion.
Spectrally-efficient relay selection with limited feedback (2008)

This paper addresses the multiplexing loss that occurs in relay networks due to causality of relays and the half-duplex constraint. We devise relay selection methods to recover the multiplexing loss in decode-and-forward (DF) relay networks, while requiring very little feedback (merely bits/relay). Two network topologies are studied: First the case is considered where a direct link is available between the source and destination, in addition to the relayed links. For this configuration, an incremental transmission scheme is proposed, and comprehensively analyzed, which uses limited feedback to improve both diversity as well as multiplexing gain. Then, the case without a direct link is considered, for which efficient non-orthogonal DF protocols are produced and analyzed. An interesting feature of the latter methods is unequal error protection capability via a family of embedded diversity-multiplexing (DMT) curves, which can be very useful for practical applications. Even considering this method's minimal DMT, a marked improvement over previous DF methods is observed, especially in high spectral efficiencies.
Quality of Data Driven Simulation Workflows (2014)

Simulations are long-running computations driven by non-trivial data dependencies. Workflow technology helps to automate these simulations and enable using Quality of Data (QoD) frameworks to determine the goodness of simulation data. However, existing frameworks are specific to scientific domains, individual applications, or proprietary workflow engine extensions. In this paper, we propose a generic approach to use QoD as a uniform means to steer complex interdisciplinary simulations implemented as workflows. The approach enables scientists to specify abstract QoD requirements that are considered to steer the workflow for ensuring a precise final result. To realize these Quality of Data-driven workflows, we present a middleware architecture and a WS-Policy-based language to describe QoD requirements and capabilities. To prove technical feasibility, we present a prototype for controlling and steering simulation workflows and a real world simulation scenario.
Metal‐Induced Decarboxylation of Diketene—A Novel Route to Allene Complexes[1] (1982)

Abstract The complete manuscript of this communication appears in: Angew. Chem. Suppl. 1982 , 1223. DOI: 10.1002/anie.198212230
Metal Artifact Reduction With MAVRIC SL at 3-T MRI in Patients With Hip Arthroplasty (2014)

The MAVRIC SL sequence can significantly reduce metal artifact on 3-T MRI compared with the 2D FSE sequence and can increase diagnostic confidence of 3-T MRI in patients with total HA.