bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dating rice remains through phytolith carbon-14 study reveals domestication at the beginning of the Holocene
Authors: Zuo Xinxin , Lu Houyuan , Jiang Leping , Zhang Jianping , Yang Xiaoyan , Huan Xiujia , He Keyang , Wang Can , Wu Naiqin 
Published: May 2017

Significance
When the domestication of rice began in its homeland, China, is an enduring and important issue of debate for researchers from many different disciplines. Reliable chronological and robust identification criteria for rice domestication are keys to understanding the issue. Here, we first use phytolith dating to constrain the initial occupation of Shangshan, an important site with early rice remains located in the Lower Yangtze region of China. We then identify the rice phytoliths of Shangshan as partly domesticated based on their morphological characteristics. The results indicate that rice domestication may have begun at Shangshan in the Lower Yangtze during the beginning of the Holocene.
Assessing human weaning practices with calcium isotopes in tooth enamel
Authors: Tacail Théo , Thivichon-Prince Béatrice , Martin Jeremy E. , Charles Cyril , Viriot Laurent , Balter Vincent 
Published: May 2017

Significance
The practice of weaning, the dietary transition from exclusive breastfeeding to exclusive nonmilk food, is a key aspect of development and evolution of hominins, but its study in the fossil record is hampered by a lack of unambiguous biomarkers. Ca stable isotope ratios of skeletal remains are expected to bear information about milk consumption. Here we demonstrate that modern human tooth enamel records a temporal variation of Ca isotope compositions, which is related to breastfeeding duration. Ca isotopes could be used as a biomarker for reconstruction of weaning practices in past human and fossil hominin species.
Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion
Authors: Tse Longping Victor , Klinc Kelli A. , Madigan Victoria J. , Castellanos Rivera Ruth M. , Wells Lindsey F. , Havlik L. Patrick , Smith J. Kennon , Agbandje-McKenna Mavis , Asokan Aravind 
Published: May 2017

Significance
Preexisting neutralizing antibodies (NAbs) against adeno-associated viruses (AAVs) pose a major, unresolved challenge that restricts patient enrollment in gene therapy clinical trials using recombinant AAV vectors. To tackle this problem, we developed a structure-guided approach to evolve AAV variants with altered antigenic footprints that cannot be recognized by preexisting antibodies. These proof-of-principle studies demonstrate that synthetic AAV variants can be evolved to evade neutralizing sera from different species—mice, nonhuman primates, and humans—without compromising yield and transduction efficiency or altering tropism. Our approach provides a roadmap for engineering any AAV strain to evade NAbs in prospective patients for human gene therapy.
Feature reassembly in the acquisition of plural marking by Korean and Indonesian bilinguals
Authors: Lee Eunji , Lardiere Donna 
Published: May 2017

This bidirectional study investigated the L2 acquisition of plural marking in L2 Indonesian by native Korean speakers and in L2 Korean by native Indonesian speakers. Indonesian and Korean are classifier languages with partially overlapping restrictions on how pluralization interacts with quantification, allowing us to test the acquisition of new L2 features vs. the preemption of L1 features that are not in the L2. We also examined how the contextual complexity of new L2 features impacts development. Seventy learners at three L2 Korean proficiency levels and 40 native controls participated in Experiment 1; 61 learners at three L2 Indonesian proficiency levels and 39 native controls participated in Experiment 2. All participants completed three tasks – a Sentence Completion Task, a Grammaticality Judgment Task and a Multiple-Choice Task. Whereas learners were largely able to overcome the difficulty of preemption, they were less successful in acquiring new L2 feature contrasts in more complex conditioning environments.
Processing DOM in relative clauses
Authors: Sagarra Nuria , Sánchez Liliana , Bel Aurora 
Published: May 2017

AbstractEarly heritage bilinguals have been repeatedly found to differ from late bilinguals and from monolinguals (e.g.,Montrul, 2008,2011). In the realm of Spanish Differential Object Marking (DOM), both early heritage bilinguals (Montrul et al., 2015) and late bilinguals (e.g.,Bowles & Montrul, 2008;Guijarro-Fuentes, 2012) exhibit difficulties. DOM in a complex structure such as relative clauses (RCs) provides an ideal setting to differentiate early from late bilinguals, but it has only been explored offline (Perpiñán & Moreno-Villar, 2013). This study fills this gap by examining the role of word order (SVO, OSV, OVS), optionality (obligatory vs. optional contexts), and saliency (bound vs. unbound morphology) on the processing of DOM in embedded RCs in Spanish, by Spanish monolinguals, and advanced early heritage and late bilinguals of Spanish. The results of a word-by-word non-cumulative self-paced reading task revealed that all participants were more accurate but were slower in subject than object RCs, and in OSV than OVS RCs. Slower RTs in subject RCs were due to the presence of DOM, and in OSV to interpreting OVS as SVO. Also, all participants were both more accurate as well as faster in obligatory than optional DOM, unbound than bound morphology, and masculine than feminine RC NPs. These findings reveal that processing difficulties in RCs result from the interaction of word order and DOM, and that processing DOM depends on both salience and, to a lesser extent, gender. Finally, this study shows that early heritage bilinguals are closer to monolinguals than late bilinguals in terms of morphosyntactic processing patterns.
The Addition of Graphene and Magnetite Materials in TiO2/CuO Catalyst for Enhancing Photosonocatalytic Performance and Reusability
Authors: Taufik A , Muzaki A , Saleh R 
Published: May 2017

Abstract
In the present study, TiO2/CuO with the addition of graphene and magnetite materials were investigated as a catalyst for waste water removal through the photosonocatalytic process. TiO2/CuO/graphene and Fe3O4/TiO2/CuO/graphene were synthesized by using the sol-gel method. Their physical properties were characterized by using X-ray Diffraction, Fourier Transform Infra-red Spectroscopy, Thermogravimetric Analysis, Transmission Electron Microscope, and Breneur Emmet Teller (BET) surface area analyzer. The Photosonocatalytic activity was examined under visible light irradiation and 40 kHz ultrasound frequency with methyl orange (MO) as a model of organic pollutant. Compared to photocatalytic and sonocatalytic process, photosonocatalytic activity can improve the degradation process due to a synergistic effect between photocatalytic and sonocatalytic process at the same time. The addition of graphene materials can improve the charge carrier separation and prevent recombination electron and holes. Therefore, the photosonocatalytic performance increases significantly with the addition of graphene materials. The addition of magnetite materials is not only can enhance the photosonocatalytic performance but also can improve the separation process for reuse the catalyst. The photosonocatalytic mechanism was correlated with their physical properties and visible as well as ultrasound irradiation.
Model-based branching point detection in single-cell data by K-branches clustering
Authors: Chlis Nikolaos K , Wolf F Alexander , Theis Fabian J 
Published: May 2017

Abstract

Motivation
The identification of heterogeneities in cell populations by utilizing single-cell technologies such as single-cell RNA-Seq, enables inference of cellular development and lineage trees. Several methods have been proposed for such inference from high-dimensional single-cell data. They typically assign each cell to a branch in a differentiation trajectory. However, they commonly assume specific geometries such as tree-like developmental hierarchies and lack statistically sound methods to decide on the number of branching events.

Results
We present K-Branches, a solution to the above problem by locally fitting half-lines to single-cell data, introducing a clustering algorithm similar to K-Means. These halflines are proxies for branches in the differentiation trajectory of cells. We propose a modified version of the GAP statistic for model selection, in order to decide on the number of lines that best describe the data locally. In this manner, we identify the location and number of subgroups of cells that are associated with branching events and full differentiation, respectively. We evaluate the performance of our method on single-cell RNA-Seq data describing the differentiation of myeloid progenitors during hematopoiesis, single-cell qPCR data of mouse blastocyst development, single-cell qPCR data of human myeloid monocytic leukemia and artificial data.

Availability and implementation
An R implementation of K-Branches is freely available at https://github.com/theislab/kbranches.

Supplementary information
Supplementary data are available at Bioinformatics online.
FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation
Authors: Min Byoungnam , Grigoriev Igor V , Choi In-Geol 
Published: May 2017

Abstract

Motivation
Successful genome analysis depends on the quality of gene prediction. Although fungal genome sequencing and assembly have become trivial, its annotation procedure has not been standardized yet.

Results
FunGAP predicts protein-coding genes in a fungal genome assembly. To attain high-quality gene models, this program runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences. To do this, we built a scoring function to estimate the congruency of each gene model based on known protein or domain homology.

Availability and implementation
FunGAP is written in Python script and is available in GitHub (https://github.com/CompSynBioLab-KoreaUniv/FunGAP). This software is freely available only for noncommercial users.

Supplementary information
Supplementary data are available at Bioinformatics online.
Integrative analysis of multiple genomic variables using a hierarchical Bayesian model
Authors: Schäfer Martin , Klein Hans-Ulrich , Schwender Holger 
Published: May 2017

Abstract

Motivation
Genes showing congruent differences in several genomic variables between two biological conditions are crucial to unravel causalities behind phenotypes of interest. Detecting such genes is important in biomedical research, e.g. when identifying genes responsible for cancer development. Small sample sizes common in next-generation sequencing studies are a key challenge, and there are still only very few statistical methods to analyze more than two genomic variables in an integrative, model-based way. Here, we present a novel bioinformatics approach to detect congruent differences between two biological conditions in a larger number of different measurements such as various epigenetic marks or mRNA transcript levels.

Results
We propose a coefficient quantifying the degree to which genes present consistent alterations in multiple (more than two) genomic variables when comparing samples presenting a condition of interest (e.g. cancer) to a reference group. A hierarchical Bayesian model is employed to assess uncertainty on a gene level, incorporating information on functional relationships between genes. We demonstrate the approach on different data sets containing RNA-seq gene transcripton and up to four ChIP-seq histone modification measurements. Both the coefficient-based ranking and the inference based on the model lead to a plausible prioritizing of candidate genes when analyzing multiple genomic variables.

Availability and implementation
BUGS code in the Supplement.

Supplementary information
Supplementary data are available at Bioinformatics online.
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank
Authors: Park Sang-Jun , Lee Jumin , Patel Dhilon S , Ma Hongjing , Lee Hui Sun , Jo Sunhwan , Im Wonpil 
Published: May 2017

Abstract

Motivation
Glycans play a central role in many essential biological processes. Glycan Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection and annotation of sugars and glycosidic linkages between sugar units and to proteins, all based on atomic coordinates and connectivity information. Carbohydrates can have various chemical modifications at different positions, making their chemical space much diverse. Unfortunately, current PDB files do not provide exact annotations for most carbohydrate derivatives and more than 50% of PDB glycan chains have at least one carbohydrate derivative that could not be correctly recognized by the original Glycan Reader.

Results
Glycan Reader has been improved and now identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported. CHARMM-GUI Glycan Reader is updated to generate the simulation system and input of various glycoconjugates with most sugar types and chemical modifications. It also offers a new functionality to edit the glycan structures through addition/deletion/modification of glycosylation types, sugar types, chemical modifications, glycosidic linkages, and anomeric states. The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Glycan Fragment Database in GlycanStructure.Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB.

Availability and implementation
http://www.charmm-gui.org/input/glycan and http://www.glycanstructure.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Blind Intubation through Self-pressurized, Disposable Supraglottic Airway Laryngeal Intubation Masks
Authors: Ruetzler Kurt , Guzzella Sandra Esther , Tscholl David Werner , Restin Tanja , Cribari Marco , Turan Alparslan , You Jing , Sessler Daniel I. , Seifert Burkhardt , Gaszynski Tomasz , Ganter Michael T. , Spahn Donat R. 
Published: May 2017

Abstract

Background
Supraglottic airway devices commonly are used for securing the airway during general anesthesia. Occasionally, intubation with an endotracheal tube through a supraglottic airway is indicated. Reported success rates for blind intubation range from 15 to 97%. The authors thus investigated as their primary outcome the fraction of patients who could be intubated blindly with an Air-Qsp supraglottic airway device (Mercury Medical, USA). Second, the authors investigated the influence of muscle relaxation on air leakage pressure, predictors for failed blind intubation, and associated complications of using the supraglottic airway device.

Methods
The authors enrolled 1,000 adults having elective surgery with endotracheal intubation. After routine induction of general anesthesia, a supraglottic airway device was inserted and patients were ventilated intermittently. Air leak pressure was measured before and after full muscle relaxation. Up to two blind intubation attempts were performed.

Results
The supraglottic airway provided adequate ventilation and oxygenation in 99% of cases. Blind intubation succeeded in 78% of all patients (95% CI, 75 to 81%). However, the success rate was inconsistent among the three centers (P < 0.001): 80% (95% CI, 75 to 85%) at the Institute of Anesthesia and Pain Therapy, Kantonsspital Winterthur, Winterthur, Switzerland; 41% (95% CI, 29 to 53%) at the Department of Anesthesiology and Intensive Therapy, Medical University of Lodz, Lodz, Poland; and 84% (95% CI, 80 to 88%) at the Institute of Anesthesiology, University Hospital Zurich, Zurich, Switzerland. Leak pressure before relaxation correlated reasonably well with air leak pressure after relaxation.

Conclusions
The supraglottic airway device reliably provided a good airway and allowed blind intubation in nearly 80% of patients. It is thus a reasonable initial approach to airway control. Muscle relaxation can be used safely when unparalyzed leak pressure is adequate.
Age-Related Differences in the Processing of Temporal Envelope and Spectral Cues in a Speech Segment
Authors: Goupell Matthew J. , Gaskins Casey R. , Shader Maureen J. , Walter Erin P. , Anderson Samira , Gordon-Salant Sandra 
Published: May 2017

Objectives:
As people age, they experience reduced temporal processing abilities. This results in poorer ability to understand speech, particularly for degraded input signals. Cochlear implants (CIs) convey speech information via the temporal envelopes of a spectrally degraded input signal. Because there is an increasing number of older CI users, there is a need to understand how temporal processing changes with age. Therefore, the goal of this study was to quantify age-related reduction in temporal processing abilities when attempting to discriminate words based on temporal envelope information from spectrally degraded signals.

Design:
Younger normal-hearing (YNH) and older normal-hearing (ONH) participants were presented a continuum of speech tokens that varied in silence duration between phonemes (0 to 60 ms in 10-ms steps), and were asked to identify whether the stimulus was perceived more as the word “dish” or “ditch.” Stimuli were vocoded using tonal carriers. The number of channels (1, 2, 4, 8, 16, and unprocessed) and temporal envelope low-pass filter cutoff frequency (50 and 400 Hz) were systematically varied.

Results:
For the unprocessed conditions, the YNH participants perceived the word ditch for smaller silence durations than the ONH participants, indicating that aging affects temporal processing abilities. There was no difference in performance between the unprocessed and 16-channel, 400-Hz vocoded stimuli. Decreasing the number of spectral channels caused decreased ability to distinguish dish and ditch. Decreasing the envelope cutoff frequency also caused decreased ability to distinguish dish and ditch. The overall pattern of results revealed that reductions in spectral and temporal information had a relatively larger effect on the ONH participants compared with the YNH participants.

Conclusions:
Aging reduces the ability to utilize brief temporal cues in speech segments. Reducing spectral information—as occurs in a channel vocoder and in CI speech processing strategies—forces participants to use temporal envelope information; however, older participants are less capable of utilizing this information. These results suggest that providing as much spectral and temporal speech information as possible would benefit older CI users relatively more than younger CI users. In addition, the present findings help set expectations of clinical outcomes for speech understanding performance by adult CI users as a function of age.
Evaluation of the Diabetes, Multidisciplinary, Experiential (DIAMANTE) Program for Retail Pharmacists: A Mixed-Method Study
Authors: Siaw Melanie Yee Lee , Ang Seng Wei , Lee Joyce Yu-Chia 
Published: May 2017

Introduction:
The Diabetes, Multidisciplinary, Experiential (DIAMANTE) program was established to enhance collaboration between retail pharmacists and the diabetes care team in the health institutions through interprofessional education. This article describes the program and reports on an evaluation of its impact on attitudes, knowledge, and confidence of the participants in managing diabetic patients.

Methods:
This study utilized a mixed-method design with focus group (FG), exit assessment, and survey. Ten participants were approached to complete the 2-week DIAMANTE program with hands-on training from a multidisciplinary diabetes team. In addition to an exit assessment and a pre-post online survey to assess attitudes of participants toward diabetes care, diabetes knowledge, and confidence in managing diabetic patients, FG was used to obtain the qualitative feedback of pharmacists. Feedback of the preceptors related to the program and pharmacist performance was also sought through an online survey. Survey data and FGs were analyzed using Wilcoxon signed-rank test and thematic analysis, respectively.

Results:
All participants completed the program successfully. The FGs revealed four themes: program design, participants' view on preceptors, participants' perceptions of program benefits, and program's outlook. Participants perceived the program content as comprehensive and relevant. With experiential learning, the pharmacists reported improved counseling skills and increased understanding of the roles of different healthcare members. Their knowledge and confidence in managing diabetic patients was improved (P = .008). All participants passed the exit assessment. In general, the preceptors were satisfied with the program design, assessment content, and participant performance.

Discussion:
The overall view of DIAMANTE appeared positive. The program also improved knowledge and confidence of the participants in managing diabetic patients.
Inflammatory Pseudotumor of the Temporal Bone: A Case Series
Authors: Ortlip Timothy E. , Drake Virginia E. , Raghavan Prashant , Papadimitriou John C. , Porter Neil C. , Eisenman David J. , Hertzano Ronna 
Published: May 2017

Objective:
Inflammatory pseudotumor of the temporal bone is a benign, idiopathic inflammatory process that is locally invasive and a cause of significant morbidity. This study reviews our experience with seven patients and is currently the largest series to date.

Study Design:
Retrospective review from January 1, 2014 to January 1, 2016.

Setting:
Single tertiary medical center.
Patients: There were five male and two female (n = 7) subjects with a diagnosis of temporal bone inflammatory pseudotumor. The mean age at presentation was 41 years old. The most common presenting symptoms were hearing loss (7/7) and headache (4/7). Four patients demonstrated an inflammatory aural polyp. Two patients experienced facial nerve paralysis.

Intervention(s):
Seven patients underwent computed tomography and six underwent magnetic resonance imaging. Corticosteroids and antibiotics were the initial treatment of choice. Five patients also underwent surgery. As adjuvant therapy, two patients received Rituximab, one patient received radiation, and one received mycophenolate mofetil.

Main Outcome Measure(s):
Clinical courses were followed with focus on symptoms, disease recurrence, duration, and treatment. Mean follow-up was 17.8 months.

Results:
The primary lesions demonstrated T2 hypo-intensity and enhancement as well as diffuse dural thickening on magnetic resonance imaging in five of six patients. Histopathology demonstrated chronic inflammation in the setting of hyalinized fibrosis (7/7). All the patients are currently symptomatically stable.

Conclusion:
Inflammatory pseudotumor of the temporal bone can cause devastating effects on neurological function and quality of life. Recognition of characteristic imaging and histopathology can expedite appropriate treatment. Patients may require chronic steroid therapy. Adjunctive therapy with radiation and immuno-modulation are currently being explored.