bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation
Authors: Lin Zhilong , Ren Yan , Shi Zhaomei , Zhang Keren , Yang Huanming , Liu Siqi , Hao Piliang 
Published: February 2020

RationaleHigh specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation.MethodsIn this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less‐complex Escherichia coli lysates to improve the sensitivity of detecting low‐abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry.ResultsTrypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2‐h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16‐h protocol.ConclusionsThe significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low‐abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2‐h protocol can potentially be a replacement for the traditional 16‐h protocol.
Metastable decomposition at the peptide C‐terminus: Possible use in protein identification
Authors: Wang Yang , Nakajima Etsuko , Okamura Yoshihito , Wang Danqing , Okumura Nobuaki , Takao Toshifumi 
Published: February 2020

RationaleThe b
n−1 ion of a peptide, as well as a [b
n−1 + 18] ion, can be observed not only as normal product ions, but also as prominent metastable ions in a reflectron‐embedded matrix‐assisted laser desorption ionization time‐of‐flight spectrometer. The m/z values for the peaks are slightly shifted compared with the ordinary product ions and appear as relatively broad peaks, which permits them to be discriminated from other ions.MethodsA standard protein mixture and gel‐derived proteins digested with LysN protease, which cleaves peptide linkages in proteins at the N‐terminal side of Lys residues, were examined. The collected data were used for protein identification using in‐house software, iD‐plus (http://coco.protein.osaka-u.ac.jp/id-plus/), which was developed for searching for proteins in the peptide database, based on enzyme specificity (N‐terminal Lys in this study), peptide masses and C‐terminal amino acids.ResultsThe b
n−1 as well as [b
n−1 + 18] ions were observed as broad ion peaks for all of the peptides (86 peptides) examined in this study. In silico calculations using the database of LysN digested peptides (11 969 470), created from 553 941 protein sequences (SwissProt: 2017_03), indicate that the use of no less than four peptides permits a protein to be identified without the need of any probability‐based scoring.ConclusionsThe preference for b
n−1 ion formation is probably due to the higher propensity of the C‐terminal peptide bond to be cleaved than other internal bonds. The fact that such C‐terminal fragmentation takes place for most of the peptides examined suggests that the use of an N‐terminal specific enzyme would allow the C‐terminal amino acids to be more reliably read out than other internal sequences, information that could be efficiently used for protein identification.
How to cheat the page limit
Authors: Duivesteijn Wouter , Hess Sibylle , Du Xin 
Published: February 2020

AbstractEvery conference imposing a limit on the length of submissions must deal with the problem of page limit cheating: authors tweaking the parameters of the game such that they can squeeze more content into their paper. We claim that this problem is endemic, although we lack the data to formally prove this. Instead, this paper provides a far from exhaustive summary of ways to cheat the page limit, a case study involving the papers accepted for the Research and Applied Data Science tracks at the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECMLPKDD) 2019, and a discussion of ways for program chairs to tackle this problem. Of the 130 accepted papers in these two ECMLPKDD 2019 tracks, 68 satisfied the page limit; 62 (47.7%) turned out to spill over the page limit, by up to as much as 50%. To misappropriate a phrase from Darrell Huff's “How to Lie with Statistics,” we intend for this paper not to be a manual for swindlers; instead, nefarious paper authors already know these tricks, and honest program chairs must learn them in self‐defense.This article is categorized under:
Commercial, Legal, and Ethical Issues > Fairness in Data Mining
Graft choice for isolated MPFL reconstruction: gracilis versus semitendinosus
Authors: Migliorini Filippo , Trivellas Andromahi , Driessen Arne , Quack Valentin , Tingart Markus , Eschweiler Jörg 
Published: February 2020

Abstract
Introduction
After the first patellar dislocation, most patients report damage of the medio-patellofemoral ligament (MPFL) and surgical reconstruction is required. The purpose of this study is to systematically review current evidence and to clarify the role of the gracilis and semitendinosus tendons as graft for isolated MPFL reconstruction.

Materials and methods
The present systematic review was conducted according to the PRISMA guidelines. The literature search was conducted in October 2019. All clinical trials using the semitendinosus and/or gracilis tendon grafts for isolated MPFL reconstruction in patients with patellofemoral instability were considered for inclusion. Only articles reporting a minimum of 12-month follow-up were considered. The PEDro score was used for the methodological quality assessment.

Results
Data from 1491 procedures were collected. The mean follow-up was 36.12 months. There was comparability among the patient baseline. All the scores of interests (Kujala, Tegner, Lysholm) and range of motion scored better in the semitendinosus group. Moreover, in favour of the semitendinosus group, a statistically significant reduction of the revision surgeries and re-dislocations were evidenced. Apprehension test and persistent instability sensation found any statistical correlations.

Conclusion
Isolated MPFL reconstruction through semitendinosus tendon graft performed better than the gracilis in selected patients suffering from recurrent patellofemoral instability.
Weak tangent and level sets of Takagi functions
Authors: Yu Han 
Published: February 2020

AbstractIn this paper, we study some properties of Takagi functions and their level sets. We show that for Takagi functions $$T_{a,b}$$Ta,b with parameters a, b such that ab is a root of a Littlewood polynomial, there exist large level sets. As a consequence, we show that for some parameters a, b, the Assouad dimension of graphs of $$T_{a,b}$$Ta,b is strictly larger than their upper box dimension. In particular, we can find weak tangents of those graphs with large Hausdorff dimension, larger than the upper box dimension of the graphs.
A conceptual model for unbiased calculations of invertebrate abundances from freeze core samples
Authors: Huber T. , Hauer C. 
Published: February 2020

AbstractFreeze coring is a commonly used method for the investigation of the bed sediment fauna of rivers. It is considered to produce quantitative numbers of invertebrate abundance in different depth layers. Calculations of abundance use total volume of the freeze core sample as spatial reference. This definition of sample volume is incorrect. In the present, study freeze core samples are shown to consist of two parts: (1) a cylindrical inner core in which the pore water has turned into ice and (2) all parts of sediment, which protrude from this inner core. Invertebrates are fixed only within the inner core since the protruding parts contain no pores and therefore no invertebrate habitat. In samples from gravel rivers, the protruding parts form a considerable bias, which depends on the size of the core and the coarseness of the sediment. In the present study, total volume of individual core segments varied between 97 and 248% of actual sample volume. The inner core can be measured directly to avoid the bias. The procedure is proposed for future studies to produce unbiased, comparable values of invertebrate abundance and consequently reliable data on vertical distribution.
Exploring Realistic Mathematics Education in a Flipped Classroom Context at the Tertiary Level
Authors: Fredriksen Helge 
Published: February 2020

AbstractFlipped classroom (FC) pedagogical frameworks have recently gained considerable popularity, especially at secondary school levels. However, there are rich opportunities to explore FC at tertiary levels, but progress on the area requires instructors’ attention to well-designed tasks for students’ collaborative learning. Realistic Mathematics Education (RME) provides a foundation for the development of such tasks. This article advances research on the role of task design in a FC context by considering how RME heuristics may be developed to include the out-of-class phase, where students prepare for in-class work with videos. This adaption, named flipped RME classroom design, is explored through two realizations of such a design with a group of computer engineering students during their first year of studying compulsory mathematics. Thematic analysis of the classroom observations shows that students’ modelling activity in-class is supported by the design of an out-of-class component in combination with teacher guidance of students’ modelling activity.
Aggregates, Formational Emergence, and the Focus on Practice in Stone Artifact Archaeology
Authors: Rezek Zeljko , Holdaway Simon J. , Olszewski Deborah I. , Lin Sam C. , Douglass Matthew , McPherron Shannon P. , Iovita Radu , Braun David R. , Sandgathe Dennis 
Published: February 2020

AbstractThe stone artifact record has been one of the major grounds for investigating our evolution. With the predominant focus on their morphological attributes and technological aspects of manufacture, stone artifacts and their assemblages have been analyzed as explicit measures of past behaviors, adaptations, and population histories. This analytical focus on technological and morphological appearance is one of the characteristics of the conventional approach for constructing inferences from this record. An equally persistent routine involves ascribing the emerged patterns and variability within the archaeological deposits directly to long-term central tendencies in human actions and cultural transmission. Here we re-evaluate this conventional approach. By invoking some of the known concerns and concepts about the formation of archaeological record, we introduce notions of aggregates and formational emergence to expand on the understanding of how artifacts accumulate, what these accumulations represent, and how the patterns and variability among them emerge. To infer behavior that could inform on past lifeways, we further promote a shift in the focus of analysis from the technological and morphological appearance of artifacts and assemblages to the practice of stone use. We argue for a more rigorous and multi-level inferential procedure in modeling behavioral adaptation and evolution.
Operation of a Diamond Cryogenic Detector for Low-Mass Dark Matter Searches
Authors: Canonica L. , Abdelhameed A. H. , Bauer P. , Bento A. , Bertoldo E. , Ferreiro Iachellini N. , Fuchs D. , Hauff D. , Mancuso M. , Petricca F. , Pröbst F. , Rothe J. 
Published: February 2020

AbstractDespite the multiple and convincing evidence of the existence of dark matter (DM) in our Universe, its detection is one of the most pressing questions in particle physics. As of today, there is no unambiguous hint which could clarify the particle nature of DM. For these reasons, a huge experimental effort is ongoing, trying to realize experiments which can probe the particle properties of DM. In particular, direct search experiments are trying to cover the largest possible mass range, from a few MeVs up to TeVs. Particularly suited for the sub-GeV mass region are detectors containing light nuclei, which are sensitive to the scattering of light DM candidates. Among them, we investigate a carbon-based absorber to explore DM masses down to the MeV region. Thanks to their cryogenic properties (high Debye temperature and long-lived phonon modes), carbon-based materials operated as low temperature calorimeters could reach an energy threshold in the eV range and would allow for the exploration of new parameters of the DM–nucleus cross section. Despite several proposals, the possibility of operating a carbon-based cryogenic detector is yet to be demonstrated. In this contribution, the preliminary results obtained with a diamond absorber operated with a TES temperature sensor will be reported. The potential of such a detector in the current landscape of DM searches will also be illustrated.
Split-and-Merge in Stationary Random Stirring on Lattice Torus
Authors: Ioffe Dmitry , Tóth Bálint 
Published: February 2020

AbstractWe show that in any dimension $$d\ge 1$$

d
≥
1

, the cycle-length process of stationary random stirring (or, random interchange) on the lattice torus converges to the canonical Markovian split-and-merge process with the invariant (and reversible) measure given by the Poisson–Dirichlet law $$\mathsf {PD(1)}$$

PD
(
1
)

, as the size of the system grows to infinity. In the case of transient dimensions, $$d\ge 3$$

d
≥
3

, the problem is motivated by attempts to understand the onset of long range order in quantum Heisenberg models via random loop representations of the latter.
Challenges of unculturable bacteria: environmental perspectives
Authors: Bodor Attila , Bounedjoum Naila , Vincze György Erik , Erdeiné Kis Ágnes , Laczi Krisztián , Bende Gábor , Szilágyi Árpád , Kovács Tamás , Perei Katalin , Rákhely Gábor 
Published: February 2020

AbstractEnvironmental biotechnology offers several promising techniques for the rehabilitation of polluted environments. The modern industrialized world presents novel challenges to the environmental sciences, requiring a constant development and deepening of knowledge to enable the characterization of novel pollutants and a better understanding of the bioremediation strategies as well as their limiting factors. The success of bioremediation depends heavily on the survival and activities of indigenous microbial communities and their interaction with introduced microorganisms. The majority of natural microbiomes remain uncultivated; therefore, further investigations focusing on their intrinsic functions in ecosystems are needed. In this review, we aimed to provide (a) a comprehensive overview of the presence of viable but nonculturable bacteria and yet-to-be-cultivated cells in nature and their diverse awakening strategies in response to, among other factors, signalling extracellular metabolites (autoinducers, resuscitation promoting factors, and siderophores); (b) an outline of the trends in isolating unculturable bacteria; and (c) the potential applications of these hidden players in rehabilitation processes.
Numeracy practices and vulnerability in old age: interdependencies and reciprocal effects
Authors: Zeuner Christine , Pabst Antje , Benz-Gydat Melanie 
Published: February 2020

AbstractIn this paper we discuss individual numeracy practices of older people (age cohort 65 and above), concentrating on findings concerning interdependencies of numeracy practices and vulnerability and their reciprocal effects, drawing on first results of a qualitative, explorative study entitled ‘Numeracy as social practice in the course of time’. For this paper, we examine the issue of vulnerability in relation to dimensions such as financial and economic situation, health and social embeddedness. Drawing on the concept of ‘numeracy as social practice’ according to Baker and Street (International encyclopedia of adult education and training, Pergamon Press, Oxford, 1996), we focus on the strategies of older people using numeracy practices and skills to lead independent, self-determined and autonomous lives, to experience individual life satisfaction and to avoid vulnerable situations. The findings, derived from in-depth interviews with the above-mentioned cohort, show that various meanings are attributed to numeracy practices in response to certain requirements and needs concerning personal well-being, as well as anticipating developments such as biographical transitions. We discuss how mathematical knowledge and skills are applied when transformed into individual numeracy practices. Our findings, which demonstrate the creative and meaningful use of numeracy practices according to personal needs, are then discussed within the scope of formal teaching and learning processes in basic adult education.
Photoreduction of Methylviologen in Saponite Clay: Effect of Methylviologen Adsorption Density on the Reaction Efficiency
Authors: Fujimura Takuya , Shimada Tetsuya , Sasai Ryo , Takagi Shinsuke 
Published: February 2020

AbstractTo identify the mechanisms for and to estimate the photochemical reaction efficiency of molecules in solid-state host materials is difficult. The objective of the present research was to measure the photogeneration efficiency of the methylviologen cation radical (MV+•) hosted in a semi-transparent hybrid film composed of MV2+ and saponite, a 2:1 clay mineral. MV+• is the one-electron reduced species of MV2+. MV+• was generated by UV irradiation of these films. The fluorescence intensity of MV2+ and the photogeneration efficiency of MV+• depended on the loading level of MV2+. When the loading level of MV2+ was high (75% of the cation exchange capacity (abbreviated as % CEC) of saponite), its fluorescence was reduced considerably because of the self-fluorescence quenching reaction, and the photogeneration efficiency of MV+• was relatively high (quantum yield φ = 3.5×10–2) compared to that of films with low adsorption density (10% CEC, φ = 1.1×10–2). Furthermore, when the loading level of MV2+ was very low (0.13% CEC), a self-fluorescence quenching reaction was not observed and MV+• was not generated. From these observations, one of the principal mechanisms of the self-quenching reaction and MV+• formation in saponite is the electron transfer reaction between excited MV2+ and adjacent MV2+ molecules in the ground state.
Unique continuation principles in cones under nonzero Neumann boundary conditions
Authors: Dipierro Serena , Felli Veronica , Valdinoci Enrico 
Published: February 2020

We consider an elliptic equation in a cone, endowed with (possibly inhomogeneous) Neumann conditions. The operator and the forcing terms can also allow non-Lipschitz singularities at the vertex of the cone.
In this setting, we provide unique continuation results, both in terms of interior and boundary points.
The proof relies on a suitable Almgren-type frequency formula with remainders. As a byproduct, we obtain classification results for blow-up limits.
Feasibility of vessel sealing devices in surgical excision of vascular malformations– novel approach
Authors: Hosny Ahmed Samir , Elmahrouky Ahmed , Balboula Ahmed , Yousry Marwan , Sharkawy M. 
Published: February 2020

ABSTRACT

Introduction:
Vascular malformations are localized defects in vascular morphogenesis that are believed to be caused by dysfunction in embryogenesis and vasculogenesis. However, with the development of new vessel sealing devices, surgical removal of the vascular malformations can be safely undertaken. The aim of this study was to test the feasibility of vessel sealing devices in the complete excision of vascular malformations.

Methods:
We retrospectively analyzed medical records of all patients with vascular malformation who underwent a surgical excision of vascular malformations at our institution from January 2015 to June 2018. All patients were followed up after 1 week; 1, 3, 6 months; and 1 year.

Results:
We assessed 14 patients with vascular malformation (median age, 21 years; malformation: arteriovenous, n = 5; venous, n = 7; lymphatic, n = 1; and combined, n = 1). These vascular malformations were localized in the right lower (n = 5) and left upper (n = 3) limbs, right upper limb (n = 2), head and neck (n = 3), and chest wall (n = 1). Using vessel sealing instruments, the nidus in AVM was excised, and complete excision of vascular malformations was achieved without depriving the skin of dermal blood supply. One patient died three weeks later due to secondary hemorrhage. Complication related to gangrenous skin over the patella was healed by vacuum-assisted closure therapy. Post-excision MRI after 18 months suggested recurrence in one patient.

Conclusion:
The use of vessel sealing devices was found to be feasible, for surgical excision of vascular malformations. However, further evidence from larger studies, prefereably randomized controlled trials, is required to support the routine use of these devices.

Highlights:
Crustal and Upper Mantle Shear Wave Velocity Structure of Botswana: The 3 April 2017 Central Botswana Earthquake Linked to the East African Rift System
Authors: Fadel Islam , Paulssen Hanneke , van der Meijde Mark , Kwadiba Motsamai , Ntibinyane Onkgopotse , Nyblade Andrew , Durrheim Raymond 
Published: February 2020

AbstractRayleigh wave group and phase velocity measurements obtained from ambient noise and earthquake data at 51 broadband stations were used to construct the first 3‐D crustal and upper mantle shear wave velocity model of Botswana. The model shows low crustal velocities associated with the Passarge and Nosop sedimentary basins, whereas the Kaapvaal, Zimbabwe, Maltahohe, and Congo Cratons are recognized by high mantle velocities. The lowest upper mantle shear wave velocity, beneath northeastern Botswana, is associated with the southwestern branch of the East African Rift System. This low‐velocity mantle anomaly appears to be linked to the crust of the Okavango Rift Zone and the location of the 3 April 2017
6.5 earthquake in central Botswana. We suggest that fluids or melt at the base of the crust from the southward continuation of the East African Rift Zone triggered the intraplate earthquake in an extensional tectonic setting.
Silicate Melting and Vaporization During Rocky Planet Formation
Authors: Davies E. J. , Carter P. J. , Root S. , Kraus R. G. , Spaulding D. K. , Stewart S. T. , Jacobsen S. B. 
Published: February 2020

AbstractCollisions that induce melting and vaporization can have a substantial effect on the thermal and geochemical evolution of planets. However, the thermodynamics of major minerals are not well known at the extreme conditions attained during planet formation. We obtained new data at the Sandia Z Machine and use published thermodynamic data for the major mineral forsterite (Mg
SiO
) to calculate the specific entropy in the liquid region of the principal Hugoniot. We use our calculated specific entropy of shocked forsterite, and revised entropies for shocked silica, to determine the critical impact velocities for melting or vaporization upon decompression from the shocked state to 1 bar and the triple points, which are near the pressures of the solar nebula. We also demonstrate the importance of the initial temperature on the criteria for vaporization. Applying these results to
‐body simulations of terrestrial planet formation, we find that up to 20% to 40% of the total system mass is processed through collisions with velocities that exceed the criteria for incipient vaporization at the triple point. Vaporizing collisions between small bodies are an important component of terrestrial planet formation.