bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wheelchair Mobility–Related Injuries Due to Inadvertent Lower Extremity Displacement on Footplates: Analysis of the FDA MAUDE Database From 2014 to 2018
Authors: Whitford Maureen , Mitchell Steven J. , Marzloff George E. , Zindle Jennifer K. , Richmond Mary Ann , Bogie Kath M. , Henzel M. Kristi 
Published: March 2020

Objectives
The aims of the study were to assess reports of wheelchair mobility–related injuries from inadvertent lower extremity displacement (ILED) on footplates, which were submitted to the Food and Drug Administration Manufacturer and User Facility Device Experience (MAUDE) database during 2014–2018, characterize injury types, and evaluate MAUDE data quality.

Methods
A systematic MAUDE database review was performed. Annual reports were searched using keywords: (a) “power wheelchair” and “injury” and (b) “mechanical (also known as manual) wheelchair” and “injury.” Reports related to injuries from ILED on the footplate were reviewed.

Results
Reports of 1075 wheelchair injuries were found across the review period. Twenty nine (3%) met our inclusion criteria. The most common source of reports was “manufacturer.” The wheelchair was unavailable for evaluation in 55.17% of reports. Manufacturers’ submission dates (number of days that passed after they were notified) ranged from 3 to 159. Reported injuries decreased by 60% from 2014 to 2018. The end user used a power wheelchair for all but one report. The most common injuries were single fractures, multiple fractures, wounds/cuts/infections, and amputations (in order of incidence). The most common mechanism was the foot slipping off the footplate during wheelchair mobility.

Conclusions
We observed inherent weaknesses in the MAUDE database reporting process and a concerning level of reporting bias. Although there were limited reports of injuries related to ILED on the footplate during wheelchair mobility, the injuries reported were significant. More standardized reporting of the mechanism and impact of these injuries is needed to better inform wheelchair design, prescription, and patient/family education.
Shoe Covers but Not Burnout? Making Burnout Reduction a Criteria for Centers for Medicare and Medicaid Services Funding Would Protect Patients
Authors: Wolpaw Jed T. , Adair Kathryn C. 
Published: March 2020

Abstract
In the United States, hospitals must meet eligibility criteria to receive federal funding. Regulatory bodies, such as the Joint Commission, are approved by the government to give, or withhold, accreditation to hospitals. This accreditation is a requisite to continue receiving funding. Hospitals are frequently cited for items such as inadequate wearing of boot covers or covering of facial hair in the operating rooms. There are very little, if any, data to support an improvement in patient safety when these items are complied with. There is, however, a large amount of data showing the negative consequences for patient safety when providers are burned out. We therefore propose that regulatory agencies such as the Joint Commission require that hospital systems measure burnout and reduce concerning levels of burnout in their employees to continue receiving certification. We briefly review evidence-based methods that hospital systems might consider to accomplish this goal.
Mutually unbiased bases containing a complex Hadamard matrix of Schmidt rank three
Authors: Hu Mengyao , Chen Lin , Sun Yize 
Published: March 2020

Constructing four six-dimensional mutually unbiased bases (MUBs) is an open problem in quantum physics and measurement. We investigate the existence of four MUBs including the identity, and a complex Hadamard matrix (CHM) of Schmidt rank three. The CHM is equivalent to a controlled unitary operation on the qubit-qutrit system via local unitary transformation
I
2
⊗
V
and
I
2
⊗
W
. We show that
V
and
W
have no zero entry, and apply it to exclude constructed examples as members of MUBs. We further show that the maximum of entangling power of controlled unitary operation is log
2
3 ebits. We derive the condition under which the maximum is achieved, and construct concrete examples. Our results describe the phenomenon that if a CHM of Schmidt rank three belongs to an MUB then its entangling power may not reach the maximum.
Dynamic aqueous multiphase reaction system for simple, sensitive and quantitative one-pot CRISPR-Cas12a based molecular diagnosis
Authors: Yin Kun , Ding Xiong , Li Ziyue , Zhao Hui , Cooper Kumarasen , Liu Changchun 
Published: March 2020

AbstractRecently, CRISPR-Cas technology has opened a new era of nucleic acid-based molecular diagnostics. However, current CRISPR-Cas-based nucleic acid biosensing has largely a lack of the quantitative detection ability and typically requires separate manual operations. Herein, we reported a dynamic aqueous multiphase reaction (DAMR) system for simple, sensitive and quantitative one-pot CRISPR-Cas12a based molecular diagnosis by taking advantage of density difference of sucrose concentration. In the DAMR system, recombinase polymerase amplification (RPA) and CRISPR-Cas12a derived fluorescent detection occurred in spatially separated but connected aqueous phases. Our DAMR system was utilized to quantitatively detect human papillomavirus (HPV) 16 and 18 DNAs with sensitivities of 10 and 100 copies within less than one hour. Multiplex detection of HPV16/18 in clinical human swab samples were successfully achieved in the DAMR system using 3D-printed microfluidic device. Furthermore, we demonstrated that target DNA in real human plasma samples can be directly amplified and detected in the DAMR system without complicated sample pre-treatment. As demonstrated, the DAMR system has shown great potential for development of next-generation point-of-care molecular diagnostics.
The O2-independent pathway of ubiquinone biosynthesis is essential for denitrification inPseudomonas aeruginosa
Authors: Vo Chau-Duy-Tam , Michaud Julie , Elsen Sylvie , Faivre Bruno , Bouveret Emmanuelle , Barras Frédéric , Fontecave Marc , Pierrel Fabien , Lombard Murielle , Pelosi Ludovic 
Published: March 2020

ABSTRACTMany proteobacteria, such asEscherichia coli, contain two main types of quinones, benzoquinones represented by ubiquinone (UQ) and naphthoquinones such as menaquinone (MK) and dimethyl-menaquinone (DMK). MK and DMK function predominantly in anaerobic respiratory chains, whereas UQ is the major electron carrier used for reduction of dioxygen. However, this division of labor is probably not so stric. Indeed, a pathway that produces UQ under anaerobic conditions in an UbiU-, UbiV- and UbiT-dependent manner has been recently discovered inE. coliwhile its physiological relevance is not yet understood because of the presence of MK and DMK in this bacterium. In the present study, we established that UQ9is the single quinone ofP. aeruginosaand that is required for growth under anaerobic respiration (denitrification). We demonstrated that ORFsPA3911, PA3912andPA3913, which are homologues to theE. coli ubiT, ubiVandubiUgenes, respectively, were essential for UQ9biosynthesis and thus for denitrification inP. aeruginosa. These three genes were hereafter calledubiTPa, ubiVPaandubiUPa. We showed that UbiVPaaccommodates a [4Fe-4S] cluster. Moreover, we demonstrated that UbiUPaand UbiTPawere able to bind UQ and that the isoprenoid tail of UQ was the structural determinant for the recognition by these Ubi proteins. Since the denitrification metabolism ofP. aeruginosais believed to be important for pathogenicity in cystic fibrosis patients, our results highlight the O2-independent UQ biosynthesis pathway as a new possible target to develop innovative antibiotics.
BCKDK regulates the TCA cycle through PDC to ensure embryonic development in the absence of PDK family
Authors: Heinemann-Yerushalmi Lia , Bentovim Lital , Felsenthal Neta , Vinestock Ron Carmel , Michaeli Nofar , Krief Sharon , Silberman Alon , Cohen Marina , Ben-Dor Shifra , Brenner Ori , Haffner-Krausz Rebecca , Itkin Maxim , Malitsky Sergey , Erez Ayelet , Zelzer Elazar 
Published: March 2020

AbstractPyruvate dehydrogenase kinases (PDK1-4) inhibit the TCA cycle by phosphorylating pyruvate dehydrogenase complex (PDC). Here, we show that the PDK family is dispensable for the survival of murine embryonic development and that BCKDK serves as a compensatory mechanism by inactivating PDC.First, we knocked out all fourPdkgenes one by one. Surprisingly,Pdktotal KO embryos developed and were born in expected ratios, but died by postnatal day 4 due to hypoglycemia or ketoacidosis.Finding that PDC was phosphorylated in these embryos suggested that another kinase compensates for the PDK family. Bioinformatic analysis implicated brunch chain ketoacid dehydrogenase kinase (Bckdk), a key regulator of branched chain amino acids (BCAA) catabolism. Indeed, knockout ofBckdkand thePdkfamily led to loss of PDC phosphorylation, increment in PDC activity, elevation of Pyruvate flux into the TCA and early embryonic lethality. These findings reveal a new regulatory crosstalk hardwiring BCAA and glucose catabolic pathways, which feed the TCA cycle.
Kappa but not delta or mu opioid receptors form homodimers at low membrane densities
Authors: Cechova Kristina , Lan Chenyang , Macik Matus , Barthes Nicolas P. F. , Jung Manfred , Ulbrich Maximilian H. 
Published: March 2020

AbstractOpioid receptors (ORs) have been observed as homo- and heterodimers, but it is unclear if the dimers are stable under physiological conditions, and whether monomers or dimers comprise the predominant fraction in a cell. Here we use three live-cell imaging approaches to assess dimerization of ORs at different expression levels. At high membrane densities, a split GFP assay reveals that κOR dimerizes, while μOR and δOR stay monomeric. In contrast, single-molecule imaging showed no κOR dimers at low receptor densities. To reconcile our seemingly contradictory results, we used a high-density single-molecule assay to assess membrane protein interactions at densities up to 100x higher than conventional single-molecule imaging. We observe that κOR is monomeric at low densities and forms dimers at densities that are considered physiological. In contrast, μOR and δOR stay monomeric even at the highest densities covered by our approach. The observation of long-lasting κOR dimers but not higher-order aggregates suggests that ORs dimerize through a single, specific interface.
Three Essential Resources to Improve Differential Scanning Fluorimetry (DSF) Experiments
Authors: Wu Taia , Yu Joshua , Gale-Day Zachary , Woo Amanda , Suresh Arundhati , Hornsby Michael , Gestwicki Jason E. 
Published: March 2020

AbstractDifferential Scanning Fluorimetry (DSF) is a method that enables rapid determination of a protein’s apparent melting temperature (Tma). Owing to its high throughput, DSF has found widespread application in fields ranging from structural biology to chemical screening. Yet DSF has developed two opposing reputations: one as an indispensable laboratory tool to probe protein stability, another as a frustrating platform that often fails. Here, we aim to reconcile these disparate reputations and help users perform more successful DSF experiments with three resources: an updated, interactive theoretical framework, practical tips, and online data analysis. We anticipate that these resources, made available online at DSFworld (https://gestwickilab.shinyapps.io/dsfworld/), will broaden the utility of DSF.
The physiological adaptation for the “fore-mid” four-legged walking behavior of the pygmy mole cricketXya sichuanensis
Authors: Zhang Yi , Wang Shuying , Feng Zhu-Jun , Liu Tong-Xian , Cao Chengquan 
Published: March 2020

AbstractAnimals have developed numerous specialized biological characteristics due to selective pressure from the environment. The pygmy mole cricketXya sichuanensishas well-developed saltatorial hind legs for jumping and benefits for its survival, but these legs cannot be used for walking. Therefore, the typical tripedal gait used by most insects with six legs is not possible, andX. sichuanensiswalks exclusively using its fore and mid legs. In this study, we describe a “fore-mid” walking pattern inX. sichuanensis.Further, we sought to deepen our understanding of the biological and physiological adaptations of this “four-legged” insect. We found the positions of tarsi points relative to the ground, integrated hind leg-abdomen structure, thickened ventral cuticle, and leg movements during walking to all show a unique biological adaptation. Of interest,X. sichuanensiswas observed to demonstrate four-legged walking, underlining the general theme that insects have strong plasticity at both physiological and behavioral levels. We suggest that on an evolutionary timescale,X. sichuanensishas developed behavioral characteristics such as optimized jumping behavior and a unique walking pattern alongside specialized anatomical adaptations to enable survival in a competitive environment. This study could help explain biological and physiological adaptations for insects’ behaviors with important implications for the study of diversity in insect locomotion.
Comparative analysis of seven short-reads sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing
Authors: Kim Hak-Min , Jeon Sungwon , Chung Oksung , Jun Je Hoon , Kim Hui-Su , Blazyte Asta , Lee Hwang-Yeol , Yu Youngseok , Cho Yun Sung , Bolser Dan M. , Bhak Jong 
Published: March 2020

AbstractBackgroundMGISEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI utilizing DNA nanoball and combinatorial probe anchor synthesis technologies for generating short reads at a very large scale – up to 60 human genomes per day. However, it has not been objectively and systematically compared against Illumina short-read sequencers.FindingsBy using the same KOREF sample, the Korean Reference Genome, we have compared seven sequencing platforms including BGISEQ-500, MGISEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000. We measured sequencing quality by comparing sequencing statistics (base quality, duplication rate, and random error rate), mapping statistics (mapping rate, depth distribution, and %GC coverage), and variant statistics (transition/transversion ratio, dbSNP annotation rate, and concordance rate with SNP genotyping chip) across the seven sequencing platforms. We found that MGI platforms showed a higher concordance rate of SNP genotyping than HiSeq2000 and HiSeq4000. The similarity matrix of variant calls confirmed that the two MGI platforms have the most similar characteristics to the HiSeq2500 platform.ConclusionsOverall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, uniformity of coverage, %GC coverage, and variant accuracy, thus we conclude that the MGI platforms can be used for a wide range of genomics research fields at approximately half the cost of the Illumina platforms.
Evaluation of biodiversity in estuaries using environmental DNA metabarcoding
Authors: Ahn Hyojin , Kume Manabu , Terashima Yuki , Ye Feng , Kameyama Satoshi , Miya Masaki , Yamashita Yoh , Kasai Akihide 
Published: March 2020

AbstractBiodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river, suggesting the potential of eDNA for non-invasive assessment of aquatic biodiversity.
Cooperative genetic networks drive a mammalian cell state transition
Authors: Lackner Andreas , Sehlke Robert , Garmhausen Marius , Stirparo Giuliano Giuseppe , Huth Michelle , Titz-Teixeira Fabian , van der Lelij Petra , Ramesmayer Julia , Thomas Henry Fabian , Ralser Meryem , Santini Laura , Sarov Mihail , Stewart A. Francis , Smith Austin , Beyer Andreas , Leeb Martin 
Published: March 2020

AbstractIn the mammalian embryo, epiblast cells must exit their naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditionsin vitro. However, our understanding of the molecular cascades and gene-networks involved in the exit from naïve pluripotency remains fragmented. Here we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems-biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 knockout ESC lines predominantly manifest delays on the trajectory from naive to formative epiblast. We find that gene networks operative in ESCs are active during transition from pre- to post-implantation epiblastin utero. We identified 374 naïve-associated genes tightly connected to epiblast state and largely conserved in human ESCs and primate embryos. Integrated analysis of mutant transcriptomes revealed funneling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signaling pathways direct this pivotal mammalian cell state transition.
Screening for functional circular RNAs using the CRISPR-Cas13 system
Authors: Li Siqi , Li Xiang , Xue Wei , Zhang Lin , Cao Shi-Meng , Lei Yun-Ni , Yang Liang-Zhong , Guo Si-Kun , Zhang Jia-Lin , Gao Xiang , Wei Jia , Li Jinsong , Yang Li , Chen Ling-Ling 
Published: March 2020

SummaryCircular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood due to inadequate methods, such as RNAi and genome engineering, in distinguishing overlapped exons in circRNAs from those in linear cognate mRNAs1,2. Here we report that the programable RNA-guided, RNA-targeting CRISPR-Cas13, RfxCas13d, effectively and specifically discriminates circRNAs from mRNAs, using guide (g)RNAs targeting sequences spanning the back-splicing junction (BSJ) sites featured in RNA circles. Using a lentiviral library that targets sequences across BSJ sites of highly expressed human circRNAs, we show that a group of circRNAs are important for cell growth mostly in a cell-type specific manner and that a common oncogenic circRNA,circFAM120A,promotes cell proliferationin vitroandin vivoby preventingFAM120AmRNA from binding the translation inhibitor IGF2BP2 for efficient translation. Application of RfxCas13d/BSJ-gRNA screening has also uncoveredcircMan1a2with regulatory potential in mouse embryo preimplantation development. Together, these results establish CRISPR-RfxCas13d as a useful tool for the discovery and functional study of circRNAs at both individual and large-scale levels.
Prioritized experience replays on a hippocampal predictive map for learning
Authors: Igata Hideyoshi , Ikegaya Yuji , Sasaki Takuya 
Published: March 2020

AbstractHippocampal cells are central to spatial and predictive representations, and experience replays by place cells are crucial for learning and memory. Nonetheless, how hippocampal replay patterns dynamically change during the learning process remains to be largely elucidated. We found that when rats updated their behavioral strategies in response to a novel salient location, place cells increased theta sequences and sharp wave ripple-associated synchronous spikes that preferentially replayed salient locations and reward-related contexts in reverse order. The directionality and contents of the replays progressively varied with learning, including an optimized path that had never been exploited by the animals. Realtime suppression of sharp wave ripples during learning inhibited the rapid stabilization of optimized behavior. Our results suggest that hippocampal replays prioritize salient experiences and support the reinforcement of new behavioral policies.One-Sentence SummaryNeuronal network mechanisms to internally rehearse learned information for updating behavioral strategy are revealed
Finding associations in a heterogeneous setting: Statistical test for aberration enrichment
Authors: Mezlini Aziz M. , Das Sudeshna , Goldenberg Anna 
Published: March 2020

AbstractMost two-group statistical tests are implicitly looking for a broad pattern such as an overall shift in mean, median or variance between the two groups. Therefore, they operate best in settings where the effect of interest is uniformly affecting everyone in one group versus the other. In real-world applications, there are many scenarios where the effect of interest is heterogeneous. For example, a drug that works very well on only a proportion of patients and is equivalent to a placebo on the remaining patients, or a disease associated gene expression dysregulation that only occurs in a proportion of cases whereas the remaining cases have expression levels indistinguishable from the controls for the considered gene. In these examples with heterogeneous effect, we believe that using classical two-group statistical tests may not be the most powerful way to detect the signal. In this paper, we developed a statistical test targeting heterogeneous effects and demonstrated its power in a controlled simulation setting compared to existing methods. We focused on the problem of finding meaningful associations in complex genetic diseases using omics data such as gene expression, miRNA expression, and DNA methylation. In simulated and real data, we showed that our test is complementary to the traditionally used statistical tests and is able to detect disease-relevant genes with heterogeneous effects which would not be detectable with previous approaches.
Whole genome bisulfite sequencing dataset of mycelium and spore of chalkbrood disease pathogenAscosphaera apis
Authors: Du Yu , Jiang Haibin , Chen Huazhi , Wang Jie , Fan Yuanchan , Fan Xiaoxue , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui 
Published: March 2020

ABSTRACTChalkbrood, a widespread fungal disease of bee larvae, is caused by the fungusAscosphaera apis. In this article, mecylia and spores ofA. apiswere respectively collected followed by DNA isolation, bisulfite conversion, cDNA library construction and next-generation sequencing. Using whole genome bisulfite sequencing (WGBS), 69,844,360 and 60,570,990 raw reads were yielded from Aam and Aas, and after quality control, 9,982,386,951 and 8,825,601,434 clean reads were obtained, respectively. In addition, 67,685,866 and 58,886,072 clean reads were mapped to the reference genome ofA. apis, including 37,643,592 and 31,568,442 unique mapped clean reads, and 49,686 and 13,348 multiple mapped clean reads. Furthermore, after bisulfite treatment, the conversion ratio of clean reads from Aam and Aas were 99.38% and 99.51%, respectively. The WGBS data ducumented here contributes to genome-wide identification of 5mC methylation sites inA. apisand comparison of methylomes between mycelium and spore.Value of the dataThis dataset can be used for genome-wide identification of 5mC methylation sites inA. apis.The accessible data could be used to systematically compare methylomes between mycelium and spore ofA. apis.Current data provides a useful resource for further study on DNA methylation-mediated mechanism underlying mycelium growth, spore germination and sexual reproduction of mycelium with the opposite sex.