bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations
Authors: Gakuhari Takashi , Nakagome Shigeki , Rasmussen Simon , Allentoft Morten E. , Sato Takehiro , Korneliussen Thorfinn , Chuinneagáin Blánaid Ní , Matsumae Hiromi , Koganebuchi Kae , Schmidt Ryan , Mizushima Souichiro , Kondo Osamu , Shigehara Nobuo , Yoneda Minoru , Kimura Ryosuke , Ishida Hajime , Masuyama Tadayuki , Yamada Yasuhiro , Tajima Atsushi , Shibata Hiroki , Toyoda Atsushi , Tsurumoto Toshiyuki , Wakebe Tetsuaki , Shitara Hiromi , Hanihara Tsunehiko , Willerslev Eske , Sikora Martin , Oota Hiroki 
Published: August 2020

AbstractAnatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.
Communication Assessment for Individuals With Minimal Verbal Skills: A Survey of Current Practices and Satisfaction
Authors: Muller Kristen , Brady Nancy C. , Fleming Kandace K. , Matthews Kris 
Published: August 2020

Purpose
There are few tools developed specifically to assess communication in people with minimal verbal skills. The literature suggests that “gold standard” assessment practice includes a combination of three components: observation, direct assessment, and indirect assessment. The purpose of this study was to describe the assessment methods practitioners and researchers currently use to measure communication skills in individuals with minimal verbal skills. We also wanted to gain information about professionals' satisfaction with their current assessment methods, as well as the factors they consider when selecting assessments for this population.

Method
A 24-question survey, composed of forced-choice, multiple-choice, Likert-type, and open-ended questions, was disseminated online using LimeSurvey. A total of 217 individuals responded to the survey. Results from the questionnaire were analyzed using qualitative and quantitative methods.

Results
The number and type of assessments used varied. Observation was the assessment method identified most frequently. Nineteen percent of the respondents reported using the gold standard approach (i.e., observation + direct + indirect). Many respondents were dissatisfied with some or many aspects of their current assessment method. Respondents who used the gold standard approach reported that their assessment method assisted in setting goals significantly better than those who did not use this approach. Comprehensiveness of skills assessed as well as ease and comfort level of the examinee were key factors in assessment selection.

Conclusions
Results from this survey suggest the need to continue to promote using multiple forms of assessment for individuals with minimal verbal skills. In addition, it points to the need to develop additional effective assessment methods for individuals with minimal verbal skills.
Comparison of Omegawave Device and an Ambulatory ECG for RR Interval
Measurement at rest
Authors: Naranjo-Orellana José , Ruso-Álvarez José Francisco , Rojo-Álvarez José Luis 
Published: August 2020

AbstractThe aim of this study was to validate the measurements of the beat intervals
taken at rest by the Omegawave® device by comparing them to
an ambulatory electrocardiogram system. For this purpose, the electrocardiogram
was digitally processed, time-aligned, and scrutinized for its suitable use as
gold-standard. Rest measurements were made for 10 minutes on 5 different days to
10 men and 3 women (24.8±5.05 years; 71.82±11.02 kg;
174.35±9.13 cm). RR intervals were simultaneously recorded using
the Omegawave device and a Holter electrocardiogram. The processing of Holter
electrocardiogram signals included the detrending of baseline noise and a
high-pass filtering for emphasizing the QRS complexes and attenuating the T
waves. After obtaining the RR intervals from the electrocardiogram, those from
the Omegawave device were automatically aligned to them with cross-correlation
digital processing techniques and compared to check whether both measurements
could be considered superimposable. A Bland-Altman analysis was applied to the 5
measurements made for all subjects. The Omegawave device exhibited very strong
agreement with a quality-controlled Holter electrocardiogram. Deviations not
exceeding 25 ms could be expected in 95% of the cases, which is
within manageable ranges both for clinical practice and for sports.
Parasympathetic Nervous Activity Responses to Different Resistance
Training Systems
Authors: Kassiano Witalo , de Vasconcelos Costa Bruna Daniella , Lima-Júnior Daltonde , Gantois Petrus , de Souza Fonseca Fabiano , da Cunha Costa Manoel , de Sousa Fortes Leonardo 
Published: August 2020

AbstractThe assessment of parasympathetic nervous activity and psychophysiological
responses infers the stress imposed by different resistance training systems.
Therefore, we compare the effects of different sets configurations, with similar
volume (~60 repetitions), on heart rate variability indices and internal
training load. Twenty-nine resistance-trained adults completed the following
conditions: traditional without and with muscle failure, inter-repetition rest,
and rest-pause in the parallel squat. The heart rate variability indices
(time-domain) were measured before and 30 min after each condition. The internal
training load was obtained through the session-rating of perceived exertion
method. Except for inter-repetition rest, all conditions reduced the heart rate
variability indices after the session (P<0.05), and the
rest-pause triggered the higher reductions (≤−46.7%).
The internal training load was higher in the rest-pause
(≤68.9%). Our results suggest that rest-pause configuration
leads to more considerable disruption of the parasympathetic nervous activity
and higher internal training load in trained adults. In contrast,
inter-repetition rest allows lower autonomic and psychophysiological stress.
Pediatric Microsurgery in the Reconstruction of Complex Posttraumatic Foot and Ankle Defects: A Long-Term Follow-Up with a Comprehensive Review of the Literature
Authors: Elbatawy Amr , Elgammal Mohammed , Zayid Tarek , Hamdy Abdelnaser , Ouf Mohamed Osama , Ismail Hany , Sholkamy Khallad , Malik Mohammad , Zidan Serag M. , Ayad Wael 
Published: August 2020

AbstractBackground Lower limb reconstruction is a well-recognized challenge to the trauma or plastic surgeon. Although techniques and outcomes in the adult population are well documented, they are less so in the pediatric population. Here, we present our experience in the management of posttraumatic foot and ankle defects with free tissue transfer in children.Methods We performed a retrospective analysis of 40 pediatric patients between the ages of 3 and 16 from 2008 to 2016 who underwent foot and ankle soft tissue reconstruction. Any patient who underwent reconstruction for any reason other than trauma was excluded. Data were collected on operative time, free tissue transfer type, use of vein grafts, length of hospital stay, and postoperative morbidity. Also, a comprehensive systematic literature review was completed according to the PRISMA protocol for all previous reports of foot and ankle reconstruction in the young age group with free tissue transfer.Results Of our 40 patients, 23 were males and 12 females, free tissue transfer was used to reconstruct primarily the dorsum (71%), heel (11%), medial (9%), and lateral (3%) aspect of the foot. The anterior tibial artery was the predominant recipient vessel for anastomosis (77%). Mean inpatient stay was 9 days and our complication rate was 20%, primarily of superficial infection treated with antibiotic therapy. The review of the literature articles is completely analyzed in detail.Conclusion The need for durable coverage of exposed joints, tendons, fractures, or hardware makes the free flap particularly well suited to trauma reconstruction of the foot and ankle. The lack of underlying vascular disease in this patient group allows for low complication rates. Our study evidences the safety and positive long-term outcomes of free tissue transfer for the reconstruction of huge sized-soft tissue defects of the foot and ankle in children.
The bounded rationality of probability distortion
Authors: Zhang Hang , Ren Xiangjuan , Maloney Laurence T. 
Published: August 2020

SignificancePeople distort probability in decision under risk and many other tasks. These distortions can be large, leading us to make markedly suboptimal decisions. There is no agreement on why we distort probability. Distortion changes systematically with task, hinting that distortions are dynamic compensations for some intrinsic “bound” on working memory. We first develop a model of the bound and compensation process and then report an experiment showing that the model accounts for individual human performance in decision under risk and relative frequency judgments. Last, we show that the particular compensation in each experimental condition serves to maximize the mutual information between objective decision variables and their internal representations. We distort probability to compensate for our own perceptual and cognitive limitations.
How cholesterol stiffens unsaturated lipid membranes
Authors: Chakraborty Saptarshi , Doktorova Milka , Molugu Trivikram R. , Heberle Frederick A. , Scott Haden L. , Dzikovski Boris , Nagao Michihiro , Stingaciu Laura-Roxana , Standaert Robert F. , Barrera Francisco N. , Katsaras John , Khelashvili George , Brown Michael F. , Ashkar Rana 
Published: August 2020

Significance
Cholesterol regulates critical cell functions, including lysis, viral budding, and antibiotic resistance, by modifying the bending rigidity of cell membranes; i.e., the ability of membranes to bend or withstand mechanical stresses. A molecular-level understanding of these functions requires knowledge of how cholesterol modifies membrane mechanics over relevant length and time scales. Currently, it is widely accepted that cholesterol has no effect on the mechanical properties of unsaturated lipid membranes, implying that viruses, for example, can bud from regions enriched in (poly)unsaturated lipids. Our observations that cholesterol causes local stiffening in DOPC membranes indicate that a reassessment of existing concepts is necessary. These findings have far-reaching implications in understanding cholesterol’s role in biology and its applications in bioengineering and drug design.
An enumerative algorithm for de novo design of proteins with diverse pocket structures
Authors: Basanta Benjamin , Bick Matthew J. , Bera Asim K. , Norn Christoffer , Chow Cameron M. , Carter Lauren P. , Goreshnik Inna , Dimaio Frank , Baker David 
Published: August 2020

Significance
Reengineering naturally occurring proteins to have new functions has had considerable impact on industrial and biomedical applications, but is limited by the finite number of known proteins. A promise of de novo protein design is to generate a larger and more diverse set of protein structures than is currently available. This vision has not yet been realized for small-molecule binder or enzyme design due to the complexity of pocket-containing structures. Here we present an algorithm that systematically generates NTF2-like protein structures with diverse pocket geometries. The scaffold sets, the insights gained from detailed structural characterization, and the computational method for generating unlimited numbers of structures should contribute to a new generation of de novo small-molecule binding proteins and catalysts.
Structural base for the transfer of GPI-anchored glycoproteins into fungal cell walls
Authors: Vogt Marian Samuel , Schmitz Gesa Felicitas , Varón Silva Daniel , Mösch Hans-Ulrich , Essen Lars-Oliver 
Published: August 2020

Significance
The synthesis and maturation of the cell wall are essential for fungal life. Factors involved in these processes provide a potential platform with side effect-free, antimycotic targets. A key step in cell-wall biogenesis is the transfer of GPI-anchored proteins from the plasma membrane to the glycan meshwork as catalyzed by Dfg5 enzymes. We characterize the structure of a member of the Dfg5 subfamily and provide insights into the architecture of the GPI-core glycan when bound to Dfg5 as supported by MD simulations and in vivo analysis in yeast. Our data let us propose a sorting mechanism at the fungal cell surface and set a base for structure-based drug development using this important cell-wall biosynthesis factor.
Human epidermal stem cell differentiation is modulated by specific lipid subspecies
Authors: Vietri Rudan Matteo , Mishra Ajay , Klose Christian , Eggert Ulrike S. , Watt Fiona M. 
Published: August 2020

Significance
Cells generate a vast repertoire of lipid molecules whose functions are poorly understood. To investigate whether lipids can regulate cell fate decisions, we carried out a systematic lipidomic analysis and perturbation of lipid metabolism in cultured human epidermal keratinocytes, determining associations with the onset of differentiation. We identified individual lipid species that induced exit from the epidermal stem cell compartment. Our observations suggest that more research is warranted on the regulation of biological processes via lipid species, moving beyond the more conventional contribution of proteins and nucleic acids.
Configurational entropy of basaltic melts in Earth’s mantle
Authors: Lee Sung Keun , Mosenfelder Jed L. , Park Sun Young , Lee A. Chim , Asimow Paul D. 
Published: August 2020

Significance
Proper inference of the seismological and chemical effects of partial melting in Earth’s upper mantle depends on physical properties of interstitial melts at elevated pressure. Silicate liquids display anomalous softening upon compression. This lacks an atomic-scale explanation, partly because studies linking microstructure and physical properties of melts are limited to ambient pressure. Here we studied basaltic glass quenched from high pressure with multinuclear NMR spectroscopy that defines the populations of oxygen species in the glass with sufficient precision to reveal a decrease with pressure in the configurational entropy, which we attribute to entanglement of the melt network upon densification. We explain how the configurational entropy can be used as a tool to explain the anomalous behavior of melts under compression.
Being native and being foreign
Authors: Minagawa Harumi , Nesbitt Dallas 
Published: August 2020

Abstract

Pennington and Richards (2016) argue that if the medium of instruction (MOI) is
not the native language of the instructor, lack of proficiency in the MOI could bring about a lack of confidence. This study inquired how
native Japanese as a Foreign Language (JFL) teachers at tertiary institutions in New Zealand and Australia perceive their English
proficiency, how it influences their linguistic identity, and how the fact that they are native speakers of the target language influences
their linguistic identity. Based on responses from an online questionnaire with more than 50 respondents as well as 12 follow-up individual
interviews, this study argues that their linguistic identity is not narrowly conceived around their non-nativeness in English and nativeness
in Japanese, but constructed from more multi-faceted aspects of language teacher identity formation, especially by factors pertinent to the
very nature of the tertiary teaching environment in these countries.
LncRNA TUG1 reverses LPS-induced cell apoptosis and inflammation of macrophage via targeting MiR-221-3p/SPRED2 axis
Authors: Hu Lili , Ye Hongwei , Liao Jianjun 
Published: August 2020

Abstract
This study aimed to identify the role of lncRNA TUG1 with miR-221-3p on mice with lipopolysaccharide (LPS)-induced acute respiratory distress syndrome (ARDS). Animal model was established, and lung tissue histopathologic status and permeability were detected by hematoxylin-eosin (HE) or Evans blue dye assay respectively. Levels of inflammation cytokines, lncRNA TUG1, miR-221-3p, sprouty related EVH1 domain-containing 2 (SPRED2), and phosphorylated (p)-ERK1/2 were determined by ELISA, qRT-PCR or Western blot. Pulmonary impairment and apoptosis were examined by flow cytometry. We observed that LPS up-regulated levels of tumor necrosis factor-α (TNF-α), Interleukin-1β (1L-1β), and ERK1/2 phosphorylation, and reduced SPRED2 levels, which were rescued by overexpressed lncRNA TUG1. StarBase and dual-luciferase reporter assay verified that miR-221-3p was targeted by lncRNA TUG1. MiR-221-3p could reverse the effect of lncRNA TUG1 on cell apoptosis, levels of TNF-α, IL-1β, SPRED2, and p-ERK1/2. Therefore, overexpressed lncRNA TUG1 attenuated LPS-induced pulmonary impairment in ARDS mice via regulating miR-221-3p/SPRED2 axis.
Experimental artefacts can lead to misattribution of bioactivity from soluble mesenchymal stem cell paracrine factors to extracellular vesicles
Authors: Whittaker Thomas E. , Nagelkerke Anika , Nele Valeria , Kauscher Ulrike , Stevens Molly M. 
Published: August 2020

ABSTRACTIt has been demonstrated that some commonly used Extracellular Vesicle (EV) isolation techniques can lead to substantial contamination with non‐EV factors. Whilst it has been established that this impacts the identification of biomarkers, the impact on apparent EV bioactivity has not been explored. Extracellular vesicles have been implicated as critical mediators of therapeutic human mesenchymal stem cell (hMSC) paracrine signalling. Isolated hMSC‐EVs have been used to treat multiple in vitro and in vivo models of tissue damage. However, the relative contributions of EVs and non‐EV factors have not been directly compared. The dependence of hMSC paracrine signalling on EVs was first established by ultrafiltration of hMSC‐conditioned medium to deplete EVs, which led to a loss of signalling activity. Here, we show that this method also causes depletion of non‐EV factors, and that when this is prevented proangiogenic signalling activity is fully restored in vitro. Subsequently, we used size‐exclusion chromatography (SEC) to separate EVs and soluble proteins to directly and quantitatively compare their relative contributions to signalling. Non‐EV factors were found to be necessary and sufficient for the stimulation of angiogenesis and wound healing in vitro. EVs in isolation were found to be capable of potentiating signalling only when isolated by a low‐purity method, or when used at comparatively high concentrations. These results indicate a potential for contaminating soluble factors to artefactually increase the apparent bioactivity of EV isolates and could have implications for future studies on the biological roles of EVs.
Recreation ecology research in China’s protected areas: progress and prospect
Authors: Zhong Linsheng , Zhang Xiangju , Deng Jinyang , Pierskalla Chad 
Published: August 2020

ABSTRACT
As a type of tourist destination, Protected Areas (PAs) have been the focus of recreation ecology research since their establishment. The contradiction between recreation and ecological protection of PAs in China is more prominent than in other countries because of China’s large population density and complex PA management system. Thus, a review of related research is urgent for promoting sustainable tourism development of PAs in China. Combining quantitative analysis with a literature review, this study analyzed the historical development process and current research topics of recreation ecology in China’s PAs, focusing on the impacts of tourism on the natural environment, environmental management of tourism, and the development of different types of sustainable tourism in PAs. Overall, the research gaps are as follows: (1) studies on impact mechanism of tourism based on long-term monitoring are lacking; (2) the existence of numerous local communities in most of the PAs in China is usually ignored; (3) insufficient attention has been paid to the impacts of tourism infrastructure construction; (4) assessments of sustainable PA tourism are lacking. Correspondingly, this paper presents implications for future research and serves as a reference for PA tourism management in other countries.
pH-responsive SERS substrates based on AgNP-polyMETAC composites on patterned self-assembled monolayers
Authors: Wang Limin , Wei Peng , Stumpf Steffi , Schubert Ulrich S , Hoeppener Stephanie 
Published: August 2020

Abstract
Patterned silver nanoparticle (NP)-poly[2-(methacryloyloxy)ethyl] trimethyl ammonium chloride (AgNP-polyMETAC) composites were prepared by electrochemical lithography, surface-initiated atom-transfer radical polymerization (SI-ATRP) and NP growth inside the polymer brushes. For this purpose, polymer brushes of poly[2-(methacryloyloxy)ethyl] trimethyl ammonium chloride (polyMETAC) were utilized as strong electrolyte brush system. These were introduced in form of patterned polymer brushes to create pH-responsive surface enhanced Raman scattering SERS substrates. It is well-known that the charges of strong polyelectrolyte chains are usually insensitive to pH changes, hence, rarely strong polyelectrolyte brushes have been utilized so far to study pH-responsive properties of such films. Here pH-insensitive polyMETAC brushes exhibit pH-sensitive properties and can be used as pH-responsive surfaces for SERS applications due to the embedding of AgNPs into the polymer brushes. When increasing the pH, the assembly of the AgNPs transfers from quasi two-dimensional (2D) aggregates, attaching mainly to the polymer surface, into a three-dimensional (3D) assembly, where the particles are penetrating into the brushes. These changes result in significant alterations of the SERS efficiency of the polymer brush composite. At pH 5, the enhancement of the Raman scattering approaches its maximum. The fabricated SERS substrates show a high sensitivity as well as good experimental reliability at different pH values. Moreover, electrochemical lithography was utilized to fabricate patterned SERS substrate, which allows an easy combination of multiple other functionalities in hierarchical structuring steps. In addition, the microstructure is in our studies beneficial because of a simplified and reliable characterization of the polymer brushes at defined sample areas. The introduction of the microstructured brush system is regarded moreover attractive for the development of high-throughput platforms for rapid, automated screening and analysis applications.