bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing natural variation of IRE1 expression and endoplasmic reticulum stress responses in Arabidopsis accessions
Authors: Afrin Taiaba , Seok Minye , Terry Brenna C. , Pajerowska-Mukhtar Karolina M. 
Published: November 2020

AbstractThe environmental effects shape genetic changes in the individuals within plant populations, which in turn contribute to the enhanced genetic diversity of the population as a whole. Thus, individuals within the same species can acquire and accumulate genetic differences in their genomes depending on their local environment and evolutionary history. IRE1 is a universal endoplasmic reticulum (ER) stress sensor that activates an evolutionarily conserved signalling cascade in response to biotic and abiotic stresses. Here, we selected nine different Arabidopsis accessions along with the reference ecotype Columbia-0, based on their geographical origins and differential endogenous IRE1 expression under steady-state conditions to investigate the natural variation of ER stress responses. We cloned and analysed selected upstream regulatory regions of IRE1a and IRE1b, which revealed differential levels of their inducibility. We also subjected these accessions to an array of biotic and abiotic stresses including heat, ER stress-inducing chemical tunicamycin, phytohormone salicylic acid, and pathogen infection. We measured IRE1-mediated splicing of its evolutionarily conserved downstream client as well as transcript accumulation of ER-resident chaperones and co-chaperones. Collectively, our results illustrate the expression polymorphism of a major plant stress receptor and its relationship with molecular and physiological ER stress sensitivity.
Fixed- versus mobile-bearing unicompartmental knee arthroplasty: a meta-analysis
Authors: Zhang Wenchao , Wang Jianpeng , Li Hui , Wang Wanchun , George Daniel M. , Huang Tianlong 
Published: November 2020

AbstractUnicompartmental knee arthroplasty (UKA) can be either a fixed bearing (FB) or a mobile bearing (MB) construct with controversy as to which design is superior. This question is addressed with a systematic review and meta-analysis. A literature search was performed using PubMed, Embase and the Cochrane Library. Studies were reviewed according to the inclusion and exclusion criteria developed in advance. We compared the differences in clinical and radiological outcomes between the FB and MB UKAs. Analyses were performed with the Review Manager and STATA software. A total of 17 studies involving 2612 knees were included. No significant differences were presented between the FB and MB prostheses in clinical and radiological outcomes. However, it was evident that there were differences in the modes and timing of the failures, bearing dislocation led to earlier failures in the MB prosthesis, while the FB prosthesis failed later due to polyethylene wear. There was no evidence of publication bias using the incidence of revisions. There is no significant difference between the FB and MB UKAs; however, there are differences in the modes and timing of failures.
Effective screening of SARS-CoV-2 neutralizing antibodies in patient serum using lentivirus particles pseudotyped with SARS-CoV-2 spike glycoprotein
Authors: Tandon Ritesh , Mitra Dipanwita , Sharma Poonam , McCandless Martin G. , Stray Stephen J. , Bates John T. , Marshall Gailen D. 
Published: November 2020

AbstractPseuodotyped particles have significant importance and use in virology as tools for studying the biology of highly pathogenic viruses in a lower biosafety environment. The biological, chemical, and serological studies of the recently emerged SARS-CoV-2 will be greatly aided by the development and optimization of a suitable pseudotyping system. Here, we pseudotyped the SARS-CoV-2 Spike glycoprotein (SPG) on a traditional retroviral (MMLV) as well as a third generation lentiviral (pLV) vector and tested the transduction efficiency in several mammalian cell lines expressing SARS-CoV-2 receptor hACE2. While MMLV pseudotyped the vesicular stomatitis virus G glycoprotein (VSV-G) efficiently, it could not pseudotype the full-length SPG. In contrast, pLV pseudotyped both glycoproteins efficiently; however, much higher titers of pLV-G particles were produced. Among all the tested mammalian cells, 293Ts expressing hACE2 were most efficiently transduced using the pLV-S system. The pLV-S particles were efficiently neutralized by diluted serum (>:640) from recently recovered COVID-19 patients who showed high SARS-CoV-2 specific IgM and IgG levels. In summary, pLV-S pseudotyped virus provides a valid screening tool for the presence of anti SARS-CoV-2 specific neutralizing antibodies in convalescent patient serum.
Mucosal microbiota and gene expression are associated with long-term remission after discontinuation of adalimumab in ulcerative colitis
Authors: Sakurai Toshiharu , Nishiyama Hiroki , Sakai Kazuko , De Velasco Marco A. , Nagai Tomoyuki , Komeda Yoriaki , Kashida Hiroshi , Okada Akiyoshi , Kawai Isao , Nishio Kazuto , Ogata Hiroyuki , Kudo Masatoshi 
Published: November 2020

AbstractGiven that sustained remission is the ultimate treatment goal in the management of patients with ulcerative colitis (UC), the decision to stop anti-tumor necrosis factor (anti-TNF) treatment in UC patients is difficult. The aim of this study was to evaluate mucosal microbiota and gene expression profiles associated with long-term remission after discontinuation of anti-TNF therapy. In nine UC patients who received anti-TNF therapy for 6 months, microbiota isolated from uninflamed mucosae and gene expression in inflamed and uninflamed mucosae were investigated at week 0 and at week 24. At treatment initiation, Fusobacterium sp. and Veillonella dispar were over-represented in the relapse group compared with the non-relapse group. After treatment, Dorea sp. and Lachnospira sp. were over-represented in the non-relapse group. In the relapse group only, a significant shift in gut bacterial community composition was found between week 0 and week 24. Gene expression of ALIX (PDCD6IP) and SLC9A3 was significantly higher in the non-relapse group than in the relapse group. Lastly, we used machine learning methods to identify relevant gene signatures associated with sustained remission. Statistical analyses of microbiota and expression profiles revealed differences between UC patients who did or did not keep remission after the discontinuation of TNF inhibitors.Trial registration: UMIN000020785: Evaluation of adalimumab therapy in mesalazine-resistant or -intolerant ulcerative colitis; an observational study (EARLY study).
Potential of MALDI-TOF-based serum N-glycan analysis for the diagnosis and surveillance of breast cancer
Authors: Lee Jong Won , Lee Kyungsoo , Ahn Sei Hyun , Son Byung Ho , Ko Beom Seok , Kim Hee Jeong , Chung Il Yong , Kim Jisun , Lee Woochang , Ko Myung-Su , Choi Soojeong , Chang Suhwan , Ko Chung Kon , Lee Sae Byul , Kim Dong-Chan 
Published: November 2020

AbstractMatrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based serum N-glycan analysis has gained acknowledgment for the diagnosis of breast cancer in recent years. In this study, the possibilities of expanding its application for breast cancer management and surveillance were discovered and evaluated. First, a novel MALDI-TOF platform, IDsys RT, was confirmed to be effective for breast cancer analysis, showing a maximum area under the curve of 0.91. Multiple N-glycan markers were identified and validated using this process, and they were found to be applicable for differentiating recurring breast cancer samples from healthy control or ordinary breast cancer samples. Recurrence samples were especially distinct from non-recurrence samples when N-glycan signatures were sampled in multiple time points and monitored via MALDI-TOF, throughout the therapy. These results suggested the feasibility of MALDI-TOF-based N-glycan analysis for tracking the molecular signatures of breast cancer and predicting recurrence.
Autofluorescence-based sorting removes senescent cells from mesenchymal stromal cell cultures
Authors: Bertolo Alessandro , Guerrero Julien , Stoyanov Jivko 
Published: November 2020

AbstractMesenchymal stromal cells (MSC) are used in cell therapy, but results depend on the unknown quality of cell populations. Extended culture time of MSC increases their senescent levels, leading to a critical loss of cell fitness. Here, we tested the suitability of MSC-sorting based on their FACS autofluorescence profile, for a rapid and non-invasive method of senescent cell elimination. Cells were classified in low- (LA) and high- (HA) autofluorescence groups, and results compared to the original MSC population (control). Three days after sorting, cells were screened by replicative senescence markers (cell volume, SA-β-Gal assay and gene/protein expression) and MSC differentiation assays. The transcriptional profiles of sorted MSC were also analyzed by RNA‐Seq. Compared to control, LA cells had 10% lower cell volume and autofluorescence, and 50% less SA-β-Gal + cells. Instead, HA cells had 20% higher cell volume and autofluorescence, and 120% more SA-β-Gal + cells. No changes in replicative senescence and differentiation potentials were observed between all groups. However, 68 genes (16 related to senescence) were significantly differentially expressed (DEG) between LA and other groups. Biological network of DEG identified CXCL12 as topological bottleneck. In summary, MSC sorting may have practical clinical implications to enhance the results of MSC-based therapies.
Reduced levels of biomarkers of exposure in smokers switching to the Carbon-Heated Tobacco Product 1.0: a controlled, randomized, open-label 5-day exposure trial
Authors: Tran Cam Tuan , Bosilkovska Marija , de La Bourdonnaye Guillaume , Blanc Nicolas , Haziza Christelle 
Published: November 2020

AbstractIn addition to smoking cessation, for those who would otherwise continue to smoke, replacing cigarettes with less harmful alternatives can reduce the harms of smoking. Heating instead of burning tobacco reduces, or eliminates, the formation of harmful and potentially harmful constituents (HPHC) that are found in cigarette smoke. The Carbon-Heated Tobacco Product (CHTP), a heat-not-burn tobacco product, mimics the cigarette smoking ritual. This randomized, open-label, two-arm, parallel-group, short-term confinement study tested the hypothesis that the geometric means of the BoExp levels for subjects switching to CHTP 1.0 for 5 days are lower relative to those continuing to smoke cigarettes. Biomarkers of exposure (BoExp), including nicotine, urinary excretion of mutagenic constituents (Ames test), and cytochrome P450 (CYP) 1A2 activity, were measured in blood and/or 24-h urine samples during ad libitum product use. Nicotine exposure remained at similar levels in individuals using CHTP as in those continuing to smoke cigarettes. Switching to CHTP resulted in marked decreases in all other urinary BoExp (56–97%), carboxyhemoglobin (59%), urinary mutagenic constituents, and CYP1A2 activity compared with continued cigarette smoking. Our results provide evidence of decreased exposure to 15 selected HPHCs in smokers switching from cigarettes to exclusive CHTP use.Trial registrationClinicalTrials.gov: NCT02503254; Date of first registration: 20/07/2015https://www.clinicaltrials.gov/ct2/show/NCT02503254.Study protocolStudy protocol published at:https://www.clinicaltrials.gov/ProvidedDocs/54/NCT02503254/Prot_000.pdf.
A causal role for the right angular gyrus in self-location mediated perspective taking
Authors: de Boer D. M. L. , Johnston P. J. , Kerr G. , Meinzer M. , Cleeremans A. 
Published: November 2020

AbstractRecent theories suggest that self-consciousness, in its most elementary form, is functionally disconnected from the phenomenal body. Patients with psychosis frequently misattribute their thoughts and actions to external sources; and in certain out-of-body experiences, lucid states, and dreams body-ownership is absent but self-identification is preserved. To explain these unusual experiences, we hypothesized that self-identification depends on inferring self-location at the right angular gyrus (i.e., perspective-taking). This process relates to the discrimination of self-produced signals (endogenous attention) from environmental stimulation (exogenous attention). Therefore, when this mechanism fails, this causes altered sensations and perceptions. We combined a Full-body Illusion paradigm with brain stimulation (HD-tDCS) and found a clear causal association between right angular gyrus activation and alterations in self-location (perspective-taking). Anodal versus sham HD-tDCS resulted in: a more profound out-of-body shift (with reduced sense of agency); and a weakened ability to discriminate self from other perspectives. We conclude that self-identification is mediated in the brain by inferring self-location (i.e., perspective-taking). Self-identification can be decoupled from the bodily self, explaining phenomena associated with disembodiment. These findings present novel insights into the relationship between mind and body, and may offer important future directions for treating psychosis symptoms and rehabilitation programs to aid in the recovery from a nervous system injury. The brain’s ability to locate itself might be the key mechanism for self-identification and distinguishing self from other signals (i.e., perspective-taking).
Investigation of enhanced oxidation stability of microencapsulated enzymatically produced tuna oil concentrates using complex coacervation
Authors: Xia Qiuyu , Akanbi Taiwo O. , Wang Bo , Li Rui , Liu Shucheng , Barrow Colin J. 
Published: November 2020

Tuna oil was selectively hydrolysed using Thermomyces lanuginosus lipase followed by stabilisation in gelatin–sodium hexametaphosphate complex coacervates to prepare microcapsules with enhanced oxidation stability.
Differential Diagnosis of Childhood Apraxia of Speech Compared to Other Speech Sound Disorders: A Systematic Review
Authors: Murray Elizabeth , Iuzzini-Seigel Jenya , Maas Edwin , Terband Hayo , Ballard Kirrie J. 
Published: November 2020

Purpose
The aim of this study was to determine the discriminative features that might contribute to differentiation of childhood apraxia of speech (CAS) from other speech sound disorders (SSDs).

Method
A comprehensive literature search was conducted for articles or doctoral dissertations that included ≥ 1 child with CAS and ≥ 1 child with SSD. Of 2,071 publications screened, 53 met the criteria. Articles were assessed for (a) study design and risk of bias; (b) participant characteristics and confidence in diagnosis; and (c) discriminative perceptual, acoustic, or kinematic measures. A criterion was used to identify promising studies: American Academy of Neurology study design (Class III+), replicable participant descriptions and adequate confidence in diagnosis (≥ 3), and ≥ 1 discriminative and reliable measure.

Results
Over 75% of studies were retrospective, case–control designs and/or assessed English-speaking children. Many studies did not fully describe study design and quality. No studies met the Class I (highest) quality rating according to American Academy of Neurology guidelines. CAS was mostly compared to speech delay/phonological disorder. Only six studies had diagnostic confidence ratings of 1 (best). Twenty-six studies reported discriminative perceptual measures, 14 reported discriminative acoustic markers, and four reported discriminative kinematic markers. Measures were diverse, and only two studies directly replicated previous findings. Overall, seven studies met the quality criteria, and another eight nearly met the study criteria to warrant further investigation.

Conclusions
There are no studies of the highest diagnostic quality. There are 15 studies that can contribute to further diagnostic efforts discriminating CAS from other SSDs. Future research should utilize careful diagnostic design, support replication, and adhere to standard reporting guidelines.

Supplemental Material

https://doi.org/10.23641/asha.13158149
Human Auditory-Frequency Tuning Is Sensitive to Tonal Language Experience
Authors: Liu Yin , Xu Runyi , Gong Qin 
Published: November 2020

Purpose
The aim of this study is to investigate whether human auditory frequency tuning can be influenced by tonal language experience.

Method
Perceptual tuning measured via psychophysical tuning curves and cochlear tuning derived via stimulus-frequency otoacoustic emission suppression tuning curves in 14 native speakers of a tonal language (Mandarin) were compared to those of 14 native speakers of a nontonal language (English) at 1 and 4 kHz.

Results

Group comparisons of both psychophysical tuning curves (
p
= .046) and stimulus-frequency otoacoustic emission suppression tuning curves (
p
= .007) in the 4-kHz region indicated sharper frequency tuning in the Mandarin-speaking group relative to the English-speaking group. The auditory tuning was better at the higher (4 kHz) than the lower (1 kHz) probe frequencies (
p
< .001).

Conclusions
The sharper auditory tuning in the 4-kHz cochlear region is associated with long-term tonal language (i.e., Mandarin) experience. Experience-dependent plasticity of tonal language may occur before the sound signal reaches central neural stages, as peripheral as the cochlea.
The Clear-Speech Benefit for School-Age Children: Speech-in-Noise and Speech-in-Speech Recognition
Authors: Calandruccio Lauren , Porter Heather L. , Leibold Lori J. , Buss Emily 
Published: November 2020

Purpose
Talkers often modify their speech when communicating with individuals who struggle to understand speech, such as listeners with hearing loss. This study evaluated the benefit of clear speech in school-age children and adults with normal hearing for speech-in-noise and speech-in-speech recognition.

Method

Masked sentence recognition thresholds were estimated for school-age children and adults using an adaptive procedure. In Experiment 1, the target and masker were summed and presented over a loudspeaker located directly in front of the listener. The masker was either speech-shaped noise or two-talker speech, and target sentences were produced using a clear or conversational speaking style. In Experiment 2, stimuli were presented over headphones. The two-talker speech masker was diotic (M
0
). Clear and conversational target sentences were presented either in-phase (T
0
) or out-of-phase (T
π
) between the two ears. The M
0
T
π
condition introduces a segregation cue that was expected to improve performance.

Results

For speech presented over a single loudspeaker (Experiment 1), the clear-speech benefit was independent of age for the noise masker, but it increased with age for the two-talker masker. Similar age effects for the two-talker speech masker were seen under headphones with diotic presentation (M
0
T
0
), but comparable clear-speech benefit as a function of age was observed with a binaural cue to facilitate segregation (M
0
T
π
).

Conclusions
Consistent with prior research, children showed a robust clear-speech benefit for speech-in-noise recognition. Immaturity in the ability to segregate target from masker speech may limit young children's ability to benefit from clear-speech modifications for speech-in-speech recognition under some conditions. When provided with a cue that facilitates segregation, children as young as 4–7 years of age derived a clear-speech benefit in a two-talker masker that was similar to the benefit experienced by adults.
The Ductus Venosus
Authors: Born Markus 
Published: November 2020

Background the ductus venosus (DV) is not well known in general radiology, but it plays a role in the daily work of pediatric radiologists. Consequently all general radiologists who also care for a pediatric department should be familiar with the physiological and pathological findings related to the DV. Methods: Literature research in Medline, using the keywords “ductus venosus” and “umbilical vein catheter”.
Results and conclusions In the first weeks of life the DV is regularly still patent. It should be recognized as DV and not be mistaken for a pathological portosystemic shunt.The ductus venosus is the lead structure for umbilical vein catheters. Radiologists should be able to assess the correct catheter position. Radiologically important findings of an umbilical vein catheter are mainly malposition and intrahepatic extravasation. Agenesis of the DV can lead to intra- or extrahepatic compensatory portosystemic shunts, in which as well as in the case of persistent patency of the DV, there may be the necessity for radiological-interventional or surgical occlusion.
Key points:
Citation Format
Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2
Authors: Ramachandran Ashwin , Huyke Diego A. , Sharma Eesha , Sahoo Malaya K. , Huang ChunHong , Banaei Niaz , Pinsky Benjamin A. , Santiago Juan G. 
Published: November 2020

Significance
Rapid, early-stage screening is crucial during pandemics for early identification of infected patients and control of disease spread. CRISPR biology offers new methods for rapid and accurate pathogen detection. Despite their versatility and specificity, existing CRISPR diagnostic methods suffer from the requirements of up-front nucleic acid extraction, large reagent volumes, and several manual steps—factors which prolong the process and impede use in low-resource settings. We here combine microfluidics, on-chip electric field control, and CRISPR to directly address limitations of current CRISPR diagnostic methods. We apply our method to the rapid detection of SARS-CoV-2 RNA in clinical samples. Our method takes about 35 min from raw sample to result, a significant improvement over existing nucleic acid-based diagnostic methods for COVID-19.
The near-boundary geometry of Einstein-vacuum asymptotically anti-de Sitter spacetimes
Authors: Shao Arick 
Published: November 2020

Abstract
We study the geometry of a general class of vacuum asymptotically anti-de Sitter spacetimes near the conformal boundary. In particular, the spacetime is only assumed to have finite regularity, and it is allowed to have arbitrary boundary topology and geometry. For the main results, we derive limits at the conformal boundary of various geometric quantities, and we use these limits to construct partial Fefferman–Graham expansions from the boundary. The results of this article will be applied, in upcoming papers, toward proving symmetry extension and gravity–boundary correspondence theorems for vacuum asymptotically anti-de Sitter spacetimes.
Absorption spectroscopy and Stokes polarimetry in a 87Rb vapour in the Voigt geometry with a 1.5 T external magnetic field
Authors: Ponciano-Ojeda Francisco S , Logue Fraser D , Hughes Ifan G 
Published: November 2020

Abstract
This paper provides details of a spectroscopic investigation of a thermal 87Rb atomic vapour. The experiment was conducted with an external magnetic field of 1.5 T in the Voigt geometry. Very good quantitative agreement between experimental data and theory is found for all four Stokes parameters—with RMS errors of ∼1.5% in all cases. From the fits to our experimental data a value for the magnetic field strength is extracted, along with the angle between the magnetic field and the polarisation of the light. The effects of the cell window birefringence on the optical rotation signals are characterised. This allows us to carry out precise measurements at a high field strength and arbitrary geometries, allowing further development of possible areas of application for atomic magnetometers.