bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction of a new scheme for classifying β‐turns in protein structures
Authors: Zhang Ruojing , Stahr Michael C. , Kennedy Michael A. 
Published: July 2021

AbstractProtein β‐turn classification remains an area of ongoing development in structural biology research. While the commonly used nomenclature defining type I, type II and type IV β‐turns was introduced in the 1970s and 1980s, refinements of β‐turn type definitions have been introduced as recently as 2019 by Dunbrack, Jr and co‐workers who expanded the number of β‐turn types to 18 (Shapovalov et al, PLOS Computat. Biol., 15, e1006844, 2019). Based on their analysis of 13 030 turns from 1074 ultrahigh resolution (≤1.2 Å) protein structures, they used a new clustering algorithm to expand the definitions used to classify protein β‐turns and introduced a new nomenclature system. We recently encountered a specific problem when classifying β‐turns in crystal structures of pentapeptide repeat proteins (PRPs) determined in our lab that are largely composed of β‐turns that often lie close to, but just outside of, canonical β‐turn regions. To address this problem, we devised a new scheme that merges the Klyne‐Prelog stereochemistry nomenclature and definitions with the Ramachandran plot. The resulting Klyne‐Prelog‐modified Ramachandran plot scheme defines 1296 distinct potential β‐turn classifications that cover all possible protein β‐turn space with a nomenclature that indicates the stereochemistry of i + 1 and i + 2 backbone dihedral angles. The utility of the new classification scheme was illustrated by re‐classification of the β‐turns in all known protein structures in the PRP superfamily and further assessed using a database of 16 657 high‐resolution protein structures (≤1.5 Å) from which 522 776 β‐turns were identified and classified.
Non‐pneumophila Legionella species pneumonia with orange‐coloured sputum
Authors: Asami‐Noyama Maki , Harada Misa , Murakawa Kaori , Suizu Junki , Murakawa Keita , Chikumoto Ayumi , Hamada Kazuki , Murata Yoriyuki , Oishi Keiji , Yamaji Yoshikazu , Edakuni Nobutaka , Hirano Tsunahiko , Kakugawa Tomoyuki , Matsunaga Kazuto 
Published: July 2021

AbstractWe herein report an immunocompromised patient familiar with gardening admitted to our hospital suffering from severe pneumonia caused by Legionella longbeachae. We suspected non‐pneumophila Legionella species pneumonia because of gardening habits, the negative urine antigen test and the non‐significant Gram staining results of orange‐coloured sputum. The pathogen was identified using mass spectrometry analysis of bronchoalveolar lavage fluid. It is important to perform the medical interview carefully, noting the colour of sputum and gardening habits, for diagnosis and targeted therapy of non‐pneumophila Legionella species pneumonia, even if the urine Legionella antigen test is negative.
Transthoracic placement of fiducials with ultrasound or electronic navigational bronchoscopy needle guidance by the interventional pulmonologist: A case series
Authors: Gaspard Dany , Boujaoude Ziad , Kubicek Gregory , Abouzgheib Wissam 
Published: July 2021

AbstractStereotactic body radiotherapy (SBRT) has become one of the main options for treatment of thoracic malignancies, leading to the need for more fiducial marker placement. We report cases where these fiducials were placed transthoracically by interventional pulmonologists using ultrasound (US) and electronic navigational bronchoscopy (ENB) needle guidance. Six cases were identified in the Cooper University Hospital medical records where such procedures were performed, alone or in combination with other interventions. All six patients underwent successful placement of fiducials. Concomitant bronchoscopic procedures were performed in four cases. All patients proceeded to SBRT without the need for further interventions. The overall retention rate of fiducials was 80%. No complications were noted. Fiducials' placement by interventional pulmonologists using US or ENB needle guidance is safe and effective, and may be combined with other procedures in a single setting.
Do brown trout (Salmo trutta L.) move streambed substrate?—Implications for durability and maintenance of artificial spawning habitat
Authors: Palm Daniel , Holmgren Annika , Losee James P. , Tylstedt Viktor , Hellstrom Gustav 
Published: July 2021

AbstractArtificial spawning habitat has been used to mitigate for lost habitat and to increase the abundance of salmonids, but the endurance and potential need of maintenance of these habitat improvements have not been well studied. We studied the movement of gravel, attributed to spawning activity of brown trout in a third‐order stream in northern Sweden by deploying PIT‐tagged grains of gravel on artificially constructed gravel patches. The results suggest that gravel movement was substantial and most prevalent at the central parts of the patches. As 76% of the tagged gravel was mobilized during a single spawning season, maintenance of this habitat improvement may be necessary in order to guarantee its functionality over time. This study provides a first step in guiding managers tasked with identifying factors degrading restored spawning habitat and maintenance needed.
The Impact of Stigmatization of Psoriasis, Atopic Dermatitis and Mastocytosis in Different Areas of Life—A Qualitative Interview Study
Authors: Heim-Ohmayer P. , Freiberger A. , Gedik M. , Beckmann J. , Ziehfreund S. , Zink A. , Hähl W. , Schielein M. C. 
Published: July 2021

Abstract

Background
Stereotypes and false assumptions about chronic and visible skin diseases can determine the behaviour towards affected individuals and result in stigmatization or discrimination.

Objective
The aim of this study was to analyze the perceived disease-related stigmatization of individuals with psoriasis, atopic dermatitis (AD) or mastocytosis. The study also aims to broaden people-centred knowledge of the effects of stigmatization in different areas of life, namely in everyday life, at work, in sports and in relationships.

Methods
Qualitative in-depth semi-structured interviews were conducted among individuals with either psoriasis, AD or mastocytosis. Participants were recruited via self-help networks and were asked to express their experience of stigmatization in different areas of life. All interviews were audio recorded, transcribed verbatim and evaluated based on Mayring's content analysis.

Results
In total, 24 individuals aged 19–79 years and living in Germany were included in the study—eight for each disease. Stigmatization was experienced in all three diseases in all mentioned areas of life as well as in interaction with medical professionals. Self-exclusion, negative self-perception and negative behaviour of others were the most frequent experiences with stigmatization.

Conclusion
Stigmatization, both internal and external, is an important factor contributing to the mental burden of people with chronic skin diseases. More research is needed to gain deeper insight into stigmatization and its psychological burden in various contexts to enhance people-centred care in chronic skin diseases.
CuCo LDHs Coated CuCoTe Honeycomb‐Like Nanosheets as a Novel Anode Material for Hybrid Supercapacitors
Authors: Jayababu Nagabandi , Kim Daewon 
Published: July 2021

AbstractMetal–organic frameworks derived metal chalcogenides as a new class of active materials can abolish the existing challenges in supercapacitors with their large electroactive sites and enhanced electrochemical conductivities. With its adequate conductivity and electrochemical properties, tellurium based metal chalcogenide electrodes can deliver better electrochemical performances than other chalcogenides. Herein, CuCoTe honeycomb‐like nanosheets are grown on nickel foam (CuCoTe HNSs/NF) and then CuCo layered double hydroxides are successively coated on them (CTC HLSs/NF). The CTC HLSs/NF electrode exhibits tremendous performance with its high specific capacity of 399 mAh g−1 at 7 A g−1 of current density and good capacity retention (81.3%) after 3000 cycles. Finally, CTC HLSs/NF electrode is utilized for the hybrid supercapacitor (HSC) assembly along with activated carbon coated nickel foam in an aqueous electrolyte. The fabricated HSC shows high energy density (214.7 Wh kg−1) and power density (40 kW kg−1). Moreover, the device retains 96.3% of its capacitance at the end of the 5000th cycle, showing its high stability. Owing to their unique morphology and superior electrochemical properties, the present method of fabrication and selected materials can address the issues faced by electrochemical capacitors.
Unusual Nanofractal Microparticles for Rapid Protein Capture and Release
Authors: Song Yongyang , Dong Xuefang , Shang Danyi , Zhang Xiaofei , Li Xiuling , Liang Xinmiao , Wang Shutao 
Published: July 2021

AbstractIon exchange porous microparticles are widely used for protein separation, but their totally porous structure often leads to slow diffusion rate and long separation time. Here unusual nanofractal microparticles synthesized by a strategy of electrostatic interaction regulated emulsion interfacial polymerization are demonstrated that exhibit excellent capability of rapid protein capture, release, and separation. The growth of nanostructures at nanofractal microparticle surface can be controlled by changing electrostatic repulsion between ion groups from weak to strong. The nanofractal microparticles provide a 3D contact model between ion groups and proteins, enable fast protein diffusion rate at initial capture and release stage, and realize rapid and efficient separation of similarly sized proteins as a proof of concept, superior to porous microparticles. This strategy offers an effective and general way for the synthesis of microparticles towards rapid and efficient separation in various fields of biomedicine, environment, and food.
Phase Transitions in a Perovskite Thin Film Studied by Environmental In Situ Heating Nano‐Beam Electron Diffraction
Authors: Meyer Tobias , Kressdorf Birte , Roddatis Vladimir , Hoffmann Jörg , Jooss Christian , Seibt Michael 
Published: July 2021

AbstractThe rich phase diagram of bulk Pr1−xCaxMnO3 resulting in a high tunability of physical properties gives rise to various studies related to fundamental research as well as prospective applications of the material. Importantly, as a consequence of strong correlation effects, electronic and lattice degrees of freedom are vigorously coupled. Hence, it is debatable whether such bulk phase diagrams can be transferred to inherently strained epitaxial thin films. In this paper, the structural orthorhombic to pseudo‐cubic transition for x = 0.1 is studied in ion‐beam sputtered thin films and differences to the respective bulk system are pointed out by employing in situ heating nano‐beam electron diffraction to follow the temperature dependence of lattice constants. In addition, it is demonstrated that controlling the environment during heating, that is, preventing oxygen loss, is crucial in order to avoid irreversible structural changes, which is expected to be a general problem of compounds containing volatile elements under non‐equilibrium conditions.
When you think you know: Restorative justice between a hearing faculty member and a Deaf+ student
Authors: Ramirez‐Stapleton Lissa D. , Duarte Donna L. 
Published: July 2021

AbstractStudents with disabilities are continuously challenged in the classroom by educators’ lack of knowing and these moments can lead to academic trauma. Through restorative justice practices a hearing faculty member and a Deaf+ student find common ground to unpack a challenging semester together. Using scholarly personal narrative methodology and written in four vignettes, this piece focuses on the need to be vulnerable when you do not know, the complex web of intersectional privileged and oppressed identities in the classroom and addressing head on.
Change begins with us: Culturally reflexive relationality as a path to social justice
Authors: Longerbeam Susan Diana , Chávez Alicia Fedelina 
Published: July 2021

AbstractIntercultural collaboration for transformational change in higher education conveyed us as scholar activists, one Mestiza and one Northern–Western European, on a 10‐year journey of reflexive practice, rooted in exploring and navigating underlying meanings and mores in our cultural ontologies. Using reflexivity, curiosity, and generosity, scholar practitioners purposefully crafted intercultural pathways for teaching, research, writing, and speaking, while negotiating cultural meanings, power, and inequities. We offer pragmatic approaches for intercultural reflexive collaboration in scholarship and practice, for social justice and equity in higher education and student affairs.
Faith got us through: Using scholarly personal narrative to explore spirituality and transition in a higher education graduate program
Authors: Travers Christopher S. , Gaston Miyah A. 
Published: July 2021

AbstractDrawing on scholarly personal narrative as a methodological technique, this article aims to catalog the ways in which faith served as an anchor in the transition for both a Black graduate student and faculty member in a Higher Education Administration graduate preparation program. Using the Hebrew Biblical text as a guide, the authors share their reflections on research, teaching, and service. Practical recommendations for both Higher Education faculty and graduate students are provided.
Laboratory tests on the fatigue behavior of damaged reinforced concrete beams under constant‐amplitude fatigue loading
Authors: Ouyang Xiangsen , Luo Xiaoyong , Liu Jie , Wang Jun , Zou Hongbo 
Published: July 2021

AbstractIn this study, constant‐amplitude fatigue tests were first performed on two types of reinforced concrete beams containing corroded reinforcements and carbonized concrete (involving corroded reinforcements). Then, the stiffness degradation behavior and the failure modes of these beams were analyzed. The results show that the stiffness of a beam first rapidly decreased and then slowly decreased under constant‐amplitude fatigue loading. In addition, the corrosion ratio of the reinforcement could affect the failure mode, and fatigue failure occurred in the compression zone of the concrete. Subsequently, a degradation equation of the bending stiffness for a damaged beam and a deflection equation that considers fatigue loads and accumulated damage were proposed. Furthermore, a staged linear curve for predicting the fatigue life of a reinforced concrete beam within certain corrosion ratio ranges was developed.
Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
Authors: Wu Hao , Becraft Philip W. 
Published: July 2021

AbstractThe naked endosperm1 (nkd1), naked endosperm2 (nkd2), and thick aleurone1 (thk1) genes are important regulators of maize (Zea mays L.) endosperm development. Double mutants of nkd1 and nkd2 (nkd1,2) show multiple aleurone (AL) cell layers with disrupted AL cell differentiation, whereas mutants of thk1 cause multiple cell layers of fully differentiated AL cells. Here, we conducted a comparative analysis of nkd1,2 and thk1 mutant endosperm transcriptomes to study how these factors regulate gene networks to control AL layer specification and cell differentiation. Weighted gene coexpression network analysis was incorporated with published laser capture microdissected transcriptome datasets to identify a coexpression module associated with AL development. In this module, both Nkd1,2+ and Thk1+ appear to regulate cell cycle and division, whereas Nkd1,2+, but not Thk1+, regulate auxin signaling. Further investigation of nkd1,2 differentially expressed genes combined with published putative targets of auxin response factors (ARFs) identified 61 AL‐preferential genes that may be directly activated by NKD‐modulated ARFs. All 61 genes were upregulated in nkd1,2 mutant and the enriched Gene Ontology terms suggested that they are associated with hormone crosstalk, lipid metabolism, and developmental growth. Expression of a transgenic DR5–red fluorescent protein auxin reporter was significantly higher in nkd1,2 mutant endosperm than in wild type, supporting the prediction that Nkd1,2+ negatively regulate auxin signaling in developing AL. Overall, these results suggest that Nkd1,2+ and Thk1+ may normally restrict AL development to a single cell layer by limiting cell division, and that Nkd1,2+ restrict auxin signaling in the AL to maintain normal cell patterning and differentiation processes.
Supplemental thiamine as a practical, potential way to prevent Alzheimer's disease from commencing
Authors: Fessel Jeffrey 
Published: July 2021

AbstractIt is better to attempt stopping Alzheimer's disease (AD) before it starts than trying to cure it after it has developed. A cerebral scan showing deposition of either amyloid or tau identifies those elderly persons whose cognition is currently normal but who are at risk of subsequent cognitive loss that may develop into AD. Synaptic hypometabolism is usually present in such at‐risk persons. Although inadequate adenosine triphosphate (ATP) may cause synaptic hypometabolism, that may not be the entire cause because, in fact, measurements in some of the at‐risk persons have shown normal ATP levels. Thiamine deficiency is often seen in elderly, ambulatory persons in whom thiamine levels correlate with Mini‐Mental State Examination scores. Thiamine deficiency has many consequences including hypometabolism, mitochondrial depression, oxidative stress, lactic acidosis and cerebral acidosis, amyloid deposition, tau deposition, synaptic dysfunction and abnormal neuro‐transmission, astrocyte function, and blood brain barrier integrity, all of which are features of AD. Although the clinical benefits of administering supplementary thiamine to patients with AD or mild cognitive impairment have been mixed, it is more likely to succeed at preventing the onset of cognitive loss if administered at an earlier time, when the number of aberrant biochemical pathways is far fewer. Providing a thiamine supplement to elderly persons who still have normal cognition but who have deposition of either amyloid or tau, may prevent subsequent cognitive loss and eventual dementia. A clinical trial is needed to validate that possibility.
Story-Making and Photography: The Visual Essay and Migration
Authors: Krase Jerome , Shortell Timothy 
Published: July 2021

AbstractIt can be argued that migrants express their own agency, via spatial practices, to change the meanings of the spaces and places they occupy and use. Although they are not the most powerful agents in our glocalized world, they nevertheless sometimes consciously and more often unconsciously, compete with others to visually define their micro-worlds for themselves and, therefore, for more powerful others as well (Krase & Shortell, 2015). Of course, migrants move, but they also settle and can establish more or less permanent enclaves. As students of mid- to large-scale urban change, we focus on commercial neighborhood vernacular landscapes which we argue have the greatest visual impact on observers. As we argue here, special attention should be paid to the visible products of their settlement which are enacted in local vernacular landscapes. For example, markets, places of worship, and even the patterns of dress of people on the street can serve as powerful semiotics or “markers” of change due to migration. It must be noted at the outset that social scientist, like ordinary observers, must avoid the common tendency to essentialize these visible signs that contribute to the problem of stereotyping social groups.
The CKM phase and $$ \overline{\theta} $$ in Nelson-Barr models
Authors: Valenti Alessandro , Vecchi Luca 
Published: July 2021

Abstract
We analyze the Nelson-Barr approach to the Strong CP Problem. We derive the necessary conditions in order to simultaneously reproduce the CKM phase and the quark masses. Then we quantify the irreducible contributions to the QCD topological angle, namely the corrections arising from loops of the colored fermion mediators that characterize these models. Corrections analytic in the couplings first arise at 3-loop order and are safely below current bounds; non-analytic effects are 2-loop order and decouple as the mediators exceed a few TeV. We discuss collider, electroweak, and flavor bounds and argue that most of the parameter space above the TeV scale is still allowed in models with down-type mediators, whereas other scenarios are more severely constrained. With two or more families of mediators the dominant experimental bound is due to the neutron electric dipole moment.
Cutkosky rules and unitarity (violation) in D-instanton amplitudes
Authors: Sen Ashoke 
Published: July 2021

Abstract
In perturbative amplitudes in quantum field theory and string field theory, Cutkosky rule expresses the anti-hermitian part of a Feynman diagram in terms of sum over all its cut diagrams, and this in turn is used to prove unitarity of the theory. For D-instanton contribution to a string theory amplitude, the cutting rule needed for the proof of unitarity is somewhat different; we need to sum over only those cut diagrams for which all the world-sheet boundaries ending on some particular D-instanton lie on the same side of the cut. By working with the closed string effective action, obtained after integrating out the open string modes, we prove that the D-instanton amplitudes actually satisfy these cutting rules, provided the effective action is real. The violation of unitarity in the closed string sector of two dimensional string theory can be traced to the failure of this reality condition. In the critical superstring theory, multi-instanton and multi anti-instanton amplitudes satisfy the reality condition. Contribution to the amplitudes from the instanton anti-instanton sector satisfies the reality condition if we make a specific choice of integration cycle over the configuration space of string fields, whereas contribution due to the non-BPS D-instantons will need to either vanish or have an overall real normalization in order for it to give real contribution. We use Picard-Lefschetz theory to argue that these conditions are indeed satisfied in superstring theories.
Contracting cosmologies and the swampland
Authors: Bernardo Heliudson , Brandenberger Robert 
Published: July 2021

Abstract
We consider the cosmology obtained using scalar fields with a negative potential energy, such as employed to obtain an Ekpyrotic phase of contraction. Applying the covariant entropy bound to the tower of states dictated by the distance conjecture, we find that the relative slope of the potential |V′|/|V| is bounded from below by a constant of the order one in Planck units. This is consistent with the requirement to obtain slow Ekpyrotic contraction. We also derive a refined condition on the potential which holds near local minima of a negative potential.
Dynamics of R-neutral Ramond fields in the D1-D5 SCFT
Authors: Lima A. A. , Sotkov G. M. , Stanishkov M. 
Published: July 2021

Abstract
We describe the effect of the marginal deformation of the $$ \mathcal{N} $$
N
= (4, 4) super-conformal (T4)N/SN orbifold theory on a doublet of R-neutral twisted Ramond fields, in the large-N approximation. Our analysis of their dynamics explores the explicit analytic form of the genus-zero four-point function involving two R-neutral Ramond fields and two deformation operators. We compute this correlation function with two different approaches: the Lunin-Mathur path-integral technique and the stress-tensor method. From its short distance limits, we extract the OPE structure constants and the scaling dimensions of non-BPS fields appearing in the fusion. In the deformed CFT, at second order in the deformation parameter, the two-point function of the n-twisted Ramond fields is UV-divergent. We perform an appropriate regularization, together with a renormalization of the undeformed fields, obtaining finite, well-defined corrections to their two-point functions and their bare conformal weights, for n < N. The fields with maximal twist n = N remain protected from renormalization, with vanishing anomalous dimensions.